Can AI predict epithelial lesion categories via automated analysis of cervical biopsies: The TissueNet challenge?

The French Society of Pathology (SFP) organized its first data challenge in 2020 with the help of the Health Data Hub (HDH). The organization of this event first consisted of recruiting nearly 5000 cervical biopsy slides obtained from 20 pathology centers. After ensuring that patients did not refuse to include their slides in the project, the slides were anonymized, digitized, and annotated by expert pathologists, and finally uploaded to a data challenge platform for competitors from around the world. Competing teams had to develop algorithms that could distinguish 4 diagnostic classes in cervical epithelial lesions. Among the many submissions from competitors, the best algorithms achieved an overall score close to 95%. The final part of the competition lasted only 6 weeks, and the goal of SFP and HDH is now to allow for the collection to be published in open access for the scientific community. In this report, we have performed a "post-competition analysis" of the results. We first described the algorithmic pipelines of 3 top competitors. We then analyzed several difficult cases that even the top competitors could not predict correctly. A medical committee of several expert pathologists looked for possible explanations for these erroneous results by reviewing the images, and we present their findings here targeted for a large audience of pathologists and data scientists in the field of digital pathology.

Autoimmunity affecting the biliary tract fuels the immunosurveillance of cholangiocarcinoma

Cholangiocarcinoma (CCA) results from the malignant transformation of cholangiocytes. Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are chronic diseases in which cholangiocytes are primarily damaged. Although PSC is an inflammatory condition predisposing to CCA, CCA is almost never found in the autoimmune context of PBC. Here, we hypothesized that PBC might favor CCA immunosurveillance. In preclinical murine models of cholangitis challenged with syngeneic CCA, PBC (but not PSC) reduced the frequency of CCA development and delayed tumor growth kinetics. This PBC-related effect appeared specific to CCA as it was not observed against other cancers, including hepatocellular carcinoma. The protective effect of PBC was relying on type 1 and type 2 T cell responses and, to a lesser extent, on B cells. Single-cell TCR/RNA sequencing revealed the existence of TCR clonotypes shared between the liver and CCA tumor of a PBC host. Altogether, these results evidence a mechanistic overlapping between autoimmunity and cancer immunosurveillance in the biliary tract.

BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium

The murine developing epicardium heterogeneously expresses the transcription factors TCF21 and WT1. Here, we show that this cell heterogeneity is conserved in human epicardium, regulated by BNC1 and associated with cell fate and function. Single cell RNA sequencing of epicardium derived from human pluripotent stem cells (hPSC-epi) revealed that distinct epicardial subpopulations are defined by high levels of expression for the transcription factors BNC1 or TCF21. WT1+ cells are included in the BNC1+ population, which was confirmed in human foetal hearts. THY1 emerged as a membrane marker of the TCF21 population. We show that THY1+ cells can differentiate into cardiac fibroblasts (CFs) and smooth muscle cells (SMCs), whereas THY1- cells were predominantly restricted to SMCs. Knocking down BNC1 during the establishment of the epicardial populations resulted in a homogeneous, predominantly TCF21high population. Network inference methods using transcriptomic data from the different cell lineages derived from the hPSC-epi delivered a core transcriptional network organised around WT1, TCF21 and BNC1. This study unveils a list of epicardial regulators and is a step towards engineering subpopulations of epicardial cells with selective biological activities.

Effect of zein additive on perfume evaporation

OBJECTIVE

Zein is known to have filmogen properties. We wanted to show if a zein film containing eugenol (eugenol as model) would retain the fragrances, slow their evaporation and therefore produce a long-lasting perception of perfume.

METHODS

We added corn zein to eugenol in a hydro-alcoholic solution to form a film in vitro and at the surface of the human skin. We have studied the trapping and release of eugenol from zein film by GC/MS. Also we labelled eugenol with deuterium to image specifically its distribution in the zein film using Secondary Ion Mass Spectrometry technique (NanoSIMS 50). Finally, we applied the zein/D-eugenol formulation onto skin to image the eugenol location on and in skin by SIMS (Secondary Ion Mass Spectrometry).

RESULTS

We showed that eugenol evaporation from zein film can be divided in three periods. The first period (≤2 h) corresponds to the simultaneous solvent and eugenol evaporation occurring during film formation. The second period corresponds to the continuous and slow eugenol evaporation during a few hours (about 10 h) but not to its completion. The third period (at least up to 48 h) results from the trapping of eugenol in zein film. After 24 or 48 h, trapped eugenol can be released and evaporated under mechanical deformations of the film. Moreover we showed that zein addition does not favour the eugenol penetration into viable epidermis which may cause allergenic cutaneous reaction.

CONCLUSION

The zein additive is safe to use, does not impact the olfactory perception, allows a better perception of the fragrance (long-lasting effect) in a more protective way and can be used in perfume.

Meet-U: Educating through research immersion

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.

Method for macromolecular colocalization using atomic recombination in dynamic SIMS

Localizing two or more components of assemblies in biological systems requires both continued development of fluorescence techniques and invention of entirely new techniques. Candidates for the latter include dynamic secondary ion mass spectrometry (D-SIMS). The latest generation of D-SIMS, the Cameca NanoSIMS 50, permits the localization of specific, isotopically labeled molecules and macromolecules in sections of biological material with a resolution in the tens of nanometers and with a sensitivity approaching in principle that of a single protein. Here we use two different systems, crystals of glycine and mixtures of proteins, to show that the formation of recombinant CN secondary ions under Cs bombardment can be exploited to create a new colocalization technique. We show experimentally that the formation of the recombinant (13)C(15)N secondary ion between (13)C- and (15)N-labeled macromolecules is indeed an indicator of the distance between the interacting macromolecules and on their shape. We build up a convolution model of the mixing-recombination process in D-SIMS that allows quantitative interpretations of the distance-dependent formation of the recombinant CN. Our results show that macromolecules can be colocalized if they are within 2 nm of one another. We discuss the potential advantages of this new technique for biological applications.

Promyelocytic leukemia-nuclear body formation is an early event leading to retinoic acid-induced differentiation of neuroblastoma cells

Neuroblastoma is one of the most common cancers in children. Neuroblastoma differentiation is linked to the presence of the promyelocytic leukemia (PML) protein. Retinoic acid, a powerful differentiation-inducer in vitro, is a potent agent for the treatment of neuroblastoma. Using two different human neuroblastoma cell lines, SH-SY5Y and LA-N-5, we show here that PML protein leads to the formation of nuclear bodies (PML-NB) after only 1 h of retinoic acid treatment and that this formation is mediated by the extracellular signal-regulated kinase (ERK) pathway. Inhibition of protein kinase C also leads to formation of PML-NB via the ERK pathway. Both sumoylation and phosphorylation of PML in an ERK-dependent pathway are also required for formation of PML-NB. Finally, we show that PML-NB formation in neuroblastoma cells is associated with neurite outgrowth. These results support the proposal that the formation of PML-NB is correlated with the differentiation of neuroblastoma cells.