NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Many efforts have been made to discover tumor-specific microenvironment elements (TMEs) from immunostained tissue sections. However, the identification of yet unknown but relevant TMEs from multiplex immunostained tissues remains a challenge, due to the number of markers involved (tens) and the complexity of their spatial interactions. We present NaroNet, which uses machine learning to identify and annotate known as well as novel TMEs from self-supervised embeddings of cells, organized at different levels (local cell phenotypes and cellular neighborhoods). Then it uses the abundance of TMEs to classify patients based on biological or clinical features. We validate NaroNet using synthetic patient cohorts with adjustable incidence of different TMEs and two cancer patient datasets. In both synthetic and real datasets, NaroNet unsupervisedly identifies novel TMEs, relevant for the user-defined classification task. As NaroNet requires only patient-level information, it renders state-of-the-art computational methods accessible to a broad audience, accelerating the discovery of biomarker signatures.Comment: 37 pages, 4 figure

Administration of a peptide inhibitor of alpha4-integrin inhibits the development of experimental autoimmune uveitis

Recruitment of lymphocytes into the retina and to the vitreous during the development of experimental autoimmune uveitis (EAU) is governed by factors such as the state of activation of inflammatory cells and the repertoire of adhesion molecules expressed by the local vascular endothelia. alpha4 Integrins and their receptors play an important role during homing of cells to the inflammatory site. In the present study, the effect of alpha4-integrin inhibitor on the development of EAU was investigated.Fil: Martín, Andrea P.. Universidade de Sao Paulo; BrasilFil: Vieira de Moraes, Luciana. Universidade de Sao Paulo; BrasilFil: Tadokoro, Carlos E.. Universidade de Sao Paulo; BrasilFil: Commodaro, Alessandra G.. Universidade de Sao Paulo; BrasilFil: Urrets Zavalia, Enrique. Universidad Catolica de Córdoba. Facultad de Medicina. Clinica Universitaria Reina Fabiola; ArgentinaFil: Rabinovich, Gabriel Adrián. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; ArgentinaFil: Urrets Zavalía, Julio Alberto. Universidad Catolica de Córdoba. Facultad de Medicina. Clinica Universitaria Reina Fabiola; ArgentinaFil: Rizzo, Luiz V.. Universidade de Sao Paulo; Brasil. Fundação Zerbini; BrasilFil: Serra, Horacio Marcelo. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentin

Placentation in Sigmodontinae: a rodent taxon native to South America

Background: Sigmodontinae, known as ""New World rats and mice,"" is a large subfamily of Cricetidae for which we herein provide the first comprehensive investigation of the placenta. Methods: Placentas of various gestational ages ranging from early pregnancy to near term were obtained for five genera, i.e. Necromys, Euryoryzomys, Cerradomys, Hylaeamys, and Oligoryzomys. They were investigated by means of histology, immunohistochemistry, a proliferation marker, DBA-lectin staining and transmission electron microscopy. Results: The chorioallantoic placenta was organized in a labyrinthine zone, spongy zone and decidua and an inverted yolk sac persisted until term. The chorioallantoic placenta was hemotrichorial. The interhemal barrier comprised fetal capillary endothelium and three layers of trophoblast, an outermost, cellular layer and two syncytial ones, with interspersed trophoblast giant cells (TGC). In addition, accumulations of TGC occurred below Reichert's membrane. The junctional zone contained syncytial trophoblast, proliferative cellular trophoblast, glycogen cells and TGC that were situated near to the maternal blood channels. In three of the genera, TGC were also accumulated in distinct areas at the placental periphery. PAS-positive glycogen cells derived from the junctional zone invaded the decidua. Abundant maternal uNK cells with positive response to PAS, vimentin and DBA-lectin were found in the decidua. The visceral yolk sac was completely inverted and villous. Conclusion: The general aspect of the fetal membranes in Sigmodontinae resembled that found in other cricetid rodents. Compared to murid rodents there were larger numbers of giant cells and in some genera these were seen to congregate at the periphery of the placental disk. Glycogen cells were found to invade the decidua but we did not identify trophoblast in the walls of the deeper decidual arteries. In contrast these vessels were surrounded by large numbers of uNK cells. This survey of wild-trapped specimens from five genera is a useful starting point for the study of placentation in an important subfamily of South American rodents. We note, however, that some of these rodents can be captive bred and recommend that future studies focus on the study of time dated pregnancies.This research was supported by grants from FAPESP (Proc. 07/51491-3 and\ud 09/53392-8)

Control of a hippocampal recurrent excitatory circuit by cannabinoid receptor-interacting protein Gap43

The type-1 cannabinoid receptor (CB1R) is widely expressed in excitatory and inhibitory nerve terminals, and by suppressing neurotransmitter release, its activation modulates neural circuits and brain function. While the interaction of CB1R with various intracellular proteins is thought to alter receptor signaling, the identity and role of these proteins are poorly understood.Using a highthroughput proteomic analysis complemented with an array of in vitro and in vivo approaches in the mouse brain, we report that the C-terminal, intracellular domain of CB1R interacts specifically with growth-associated protein of 43 kDa (GAP43). The CB1R-GAP43 interaction occurs selectively at mossy cell axon boutons, which establish excitatory synapses with dentate granule cells in the hippocampus. This interaction impairs CB1R-mediated suppression of mossy cell to granule cell transmission, thereby inhibiting cannabinoidmediated anti-convulsant activity inmice. Thus, GAP43 acts as a synapse typespecific regulatory partner of CB1R that hampers CB1R-mediated effects on hippocampal circuit function

Endoscopical and pathological dissociation in severe colitis induced by immune-checkpoint inhibitors

Checkpoint inhibitors have improved the survival of patients with advanced tumors and show a manageable toxicity profile. However, auto-immune colitis remains a relevant side effect, and combinations of anti-PD1/PDL1 and anti-CTLA-4 increase its incidence and severity. Here, we report the case of a 50-year-old patient diagnosed with stage IV cervical cancer that relapsed following radical surgery, external radiation/brachytherapy and standard chemotherapy. She was subsequently treated with Nivolumab and Ipilimumab combination and developed grade 2 colitis presenting a dissociation between endoscopic and pathological findings. At cycle 10 the patient reported grade 3 diarrhea and abdominal discomfort, without blood or mucus in the stools. Immunotherapy was withheld and a colonoscopy was performed, showing normal mucosa in the entire colon. Puzzlingly, histologic evaluation of randomly sampled mucosal biopsy of the distal colon showed an intense intraepithelial lymphocyte infiltration with crypt loss and some regenerating crypts with a few apoptotic bodies set in a chronically inflamed lamina propria, consistent with the microscopic diagnosis of colitis. Treatment with methylprednisolone 2 mg/kg was initiated which led to a decrease in the number of stools to grade 1. Additional investigations to exclude other causes of diarrhea rendered negative results. The patient experienced a major partial response and, following the resolution of diarrhea, she was re-challenged again with immunotherapy, with the reappearance of grade 2 diarrhea, leading to permanent immunotherapy interruption. We conclude and propose that performing random colonic biopsies should be considered in cases of immune checkpoint-associated unexplained diarrhea, even when colonoscopy shows macroscopically normal colonic mucosa inflammatory lesions

Synthesis and structure-activity analysis of new phosphonium salts with potent activity against African trypanosomes

A series of 73 bisphosphonium salts and 10 monophosphonium salt derivatives were synthesized and tested in vitro against several wild type and resistant lines of Trypanosoma brucei (T. b. rhodesiense STIB900, T. b. brucei strain 427, TbAT1-KO, and TbB48). More than half of the compounds tested showed a submicromolar EC 50 against these parasites. The compounds did not display any cross-resistance to existing diamidine therapies, such as pentamidine. In most cases, the compounds displayed a good selectivity index versus human cell lines. None of the known T. b. brucei drug transporters were required for trypanocidal activity, although some of the bisphosphonium compounds inhibited the low affinity pentamidine transporter. It was found that phosphonium drugs act slowly to clear a trypanosome population but that only a short exposure time is needed for irreversible damage to the cells. A comparative molecular field analysis model (CoMFA) was generated to gain insights into the SAR of this class of compounds, identifying key features for trypanocidal activity. © 2012 American Chemical Society.Peer Reviewe

Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury

Severe lung damage resulting from COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways, and genes present across the spectrum of histopathological damage in COVID-19–affected lung tissue. We applied correlation network–based approaches to deconvolve gene expression data from 46 areas of interest covering more than 62,000 cells within well-preserved lung samples from 3 patients. Despite substantial interpatient heterogeneity, we discovered evidence for a common immune-cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines, including CXCL9, CXCL10, and CXCL11, which are known to promote the recruitment of CXCR3+ immune cells. The TNF superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were consistently upregulated in the areas with severe tissue damage. We used published spatial and single-cell SARS-CoV-2 data sets to validate our findings in the lung tissue from additional cohorts of patients with COVID-19. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies

Antarctic ozone hole modifies iodine geochemistry on the Antarctic Plateau

Polar stratospheric ozone has decreased since the 1970s due to anthropogenic emissions of chlorofluorocarbons and halons, resulting in the formation of an ozone hole over Antarctica. The effects of the ozone hole and the associated increase in incoming UV radiation on terrestrial and marine ecosystems are well established; however, the impact on geochemical cycles of ice photoactive elements, such as iodine, remains mostly unexplored. Here, we present the first iodine record from the inner Antarctic Plateau (Dome C) that covers approximately the last 212 years (1800-2012 CE). Our results show that the iodine concentration in ice remained constant during the pre-ozone hole period (1800-1974 CE) but has declined twofold since the onset of the ozone hole era (~1975 CE), closely tracking the total ozone evolution over Antarctica. Based on ice core observations, laboratory measurements and chemistry-climate model simulations, we propose that the iodine decrease since ~1975 is caused by enhanced iodine re-emission from snowpack due to the ozone hole-driven increase in UV radiation reaching the Antarctic Plateau. These findings suggest the potential for ice core iodine records from the inner Antarctic Plateau to be as an archive for past stratospheric ozone trends.Fil: Spolaor, Andrea. Consiglio Nazionale Delle Ricerche. Istituto Di Scienze Polari.; Italia. Universita' Ca' Foscari Di Venezia; ItaliaFil: Burgay, François. Universita' Ca' Foscari Di Venezia; Italia. Paul Scherrer Institute; SuizaFil: Fernandez, Rafael Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Interdisciplinario de Ciencias Básicas. - Universidad Nacional de Cuyo. Instituto Interdisciplinario de Ciencias Básicas; ArgentinaFil: Turetta, Clara. Consiglio Nazionale Delle Ricerche. Istituto Di Scienze Polari.; Italia. Universita' Ca' Foscari Di Venezia; ItaliaFil: Cuevas, Carlos A.. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; EspañaFil: Kim, Kitae. Korea Polar Research Institute; Corea del SurFil: Kinnison, Douglas E.. National Center for Atmospheric Research; Estados UnidosFil: Lamarque, Jean-François. National Center for Atmospheric Research; Estados UnidosFil: de Blasi, Fabrizio. Consiglio Nazionale Delle Ricerche. Istituto Di Scienze Polari.; Italia. Universita' Ca' Foscari Di Venezia; ItaliaFil: Barbaro, Elena. Consiglio Nazionale Delle Ricerche. Istituto Di Scienze Polari.; Italia. Universita' Ca' Foscari Di Venezia; ItaliaFil: Corella, Juan Pablo. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; EspañaFil: Vallelonga, Paul. Universidad de Copenhagen; Dinamarca. University of Western Australia; AustraliaFil: Frezzotti, Massimo. Università Roma Tre Iii. Dipartimento Di Scienze.; ItaliaFil: Barbante, Carlo. Consiglio Nazionale Delle Ricerche. Istituto Di Scienze Polari.; Italia. Universita' Ca' Foscari Di Venezia; ItaliaFil: Saiz López, Alfonso. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; Españ

The association between the tumor immune microenvironments and clinical outcome in low-grade, early-stage endometrial cancer patients

Endometrial tumors show substantial heterogeneity in their immune microenvironment. This heterogeneity could be used to improve the accuracy of current outcome prediction tools. We assessed the immune microenvironment of 235 patients diagnosed with low-grade, early-stage endometrial cancer. Multiplex quantitative immunofluorescence was carried out tomeasure CD8, CD68, FOXP3, PD-1,and PD-L1markers, aswell as cytokeratin (CK), on tissuemicroarrays. Clustering results revealed five robust immune response patterns, each associated with specific immune populations, cell phenotypes, and cell spatial clustering.Most samples (69%) belonged to theimmune-desert subtype, characterized by lowimmune cell densities. Tumor-infiltrating lymphocyte (TIL)-rich samples (4%) displayed high CD8+ T-cell infiltration, as well as a high percentage of CD8/PD-1+ cells. Immune-exclusion samples (19%) displayed the lowest CD8+ infiltration combined with high PD-L1 expression levels in CK+ tumor cells. In addition, they demonstrated high tumor cell spatial clustering as well as increased spatial proximity of CD8+/PD-1+ andCK/PD-L1+ cells.FOXP3andmacrophage-rich phenotypes (3%and 4% of total samples) displayed relatively high levels of FOXP3+ regulatory T-cells and CD68+ macrophages, respectively. These phenotypes correlated with clinical outcomes, with immune-exclusion tumors showing an association with tumor relapse. When compared with prediction models built using routine pathological variables, models optimized with immune variables showed increased outcome prediction capacity (AUC = 0.89 versus 0.78) and stratification potential. The improved prediction capacity was independent of mismatch repair protein status and adjuvant radiotherapy treatment. Further, immunofluorescence results could be partially recapitulated using single-marker immunohistochemistry (IHC) performed on whole tissue sections. TIL-rich tumors demonstrated increased CD8+ T-cells by IHC, while immune-exclusion tumors displayed a lack of CD8+ T-cells and frequent expression of PD-L1 in tumor cells. Our results demonstrate the capability of the immune microenvironment to improve standard prediction tools in low-grade, early-stage endometrial carcinomasCEA and IgM were funded by Fundación La Marató de TV3. This project was supported by grants from Partners of Choice Network from AstraZeneca and by the Instituto de Salud Carlos III (ISCIII) (PI17/01723 and PI21/00920), co-financed by the European Regional Development Fund ‘A way to achieve Europe’ (FEDER). We thank Marco Cassano (Lunaphore Technologies) for his help in writing the manuscrip

Peripheral chondrosarcoma progression is associated with increased type X collagen and vascularisation

Endochondral bone formation requires a cartilage template, known as the growth plate, and vascular invasion, bringing osteoblasts and osteoclasts. Endochondral chondrocytes undergo sequences of cell division, matrix secretion, cell hypertrophy, apoptosis, and matrix calcification/mineralisation. In this study, two critical steps of endochondral bone formation, the deposition of collagen X-rich matrix and blood vessel attraction/invasion, were investigated by immunohistochemistry. Fourteen multiple osteochondromas and six secondary peripheral chondrosarcomas occurring in patients with multiple osteochondromas were studied and compared to epiphyseal growth plate samples. Mutation analysis showed all studied patients (expect one) to harbour a germ-line mutations in either EXT1 or EXT2. Here, we described that homozygous mutations in EXT1/EXT2, which are causative for osteochondroma formation, are likely to affect terminal chondrocyte differentiation and vascularisation in the osteocartilaginous interface. Contrastingly, terminal chondrocyte differentiation and vascularisation seem to be unaffected in secondary peripheral chondrosarcoma. In addition, osteochondromas with high vascular density displayed a higher proliferation rate. A similar apoptotic rate was observed in osteochondromas and secondary peripheral chondrosarcomas. Recently, it has been shown that cells with functional EXT1 and EXT2 are outnumbering EXT1/EXT2 mutated cells in secondary peripheral chondrosarcomas. This might explain the increased type X collagen production and blood vessel attraction in these malignant tumours