Utilizing human cerebral organoids to model breast cancer brain metastasis in culture.

BACKGROUND: Metastasis, the spread, and growth of malignant cells at secondary sites within a patient's body, accounts for over 90% of cancer-related mortality. Breast cancer is the most common tumor type diagnosed and the leading cause of cancer lethality in women in the United States. It is estimated that 10-16% breast cancer patients will have brain metastasis. Current therapies to treat patients with breast cancer brain metastasis (BCBM) remain palliative. This is largely due to our limited understanding of the fundamental molecular and cellular mechanisms through which BCBM progresses, which represents a critical barrier for the development of efficient therapies for affected breast cancer patients. METHODS: Previous research in BCBM relied on co-culture assays of tumor cells with rodent neural cells or rodent brain slice ex vivo. Given the need to overcome the obstacle for human-relevant host to study cell-cell communication in BCBM, we generated human embryonic stem cell-derived cerebral organoids to co-culture with human breast cancer cell lines. We used MDA-MB-231 and its brain metastatic derivate MDA-MB-231 Br-EGFP, other cell lines of MCF-7, HCC-1806, and SUM159PT. We leveraged this novel 3D co-culture platform to investigate the crosstalk of human breast cancer cells with neural cells in cerebral organoid. RESULTS: We found that MDA-MB-231 and SUM159PT breast cancer cells formed tumor colonies in human cerebral organoids. Moreover, MDA-MB-231 Br-EGFP cells showed increased capacity to invade and expand in human cerebral organoids. CONCLUSIONS: Our co-culture model has demonstrated a remarkable capacity to discern the brain metastatic ability of human breast cancer cells in cerebral organoids. The generation of BCBM-like structures in organoid will facilitate the study of human tumor microenvironment in culture.

Current cell therapies for systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease in which multiple organs are damaged by the immune system. Although standard treatment options such as hydroxychloroquine (HCQ), glucocorticoids (GCs), and other immunosuppressive or immune-modulating agents can help to manage symptoms, they do not offer a cure. Hence, there is an urgent need for the development of novel drugs and therapies. In recent decades, cell therapies have been used for the treatment of SLE with encouraging results. Hematopoietic stem cell transplantation, mesenchymal stem cells, regulatory T (Treg) cell, natural killer cells, and chimeric antigen receptor T (CAR T) cells are advanced cell therapies which have been developed and evaluated in clinical trials in humans. In clinical application, each of these approaches has shown advantages and disadvantages. In addition, further studies are necessary to conclusively establish the safety and efficacy of these therapies. This review provides a summary of recent clinical trials investigating cell therapies for SLE treatment, along with a discussion on the potential of other cell-based therapies. The factors influencing the selection of common cell therapies for individual patients are also highlighted.

Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids.

The human blood-brain barrier (hBBB) is a highly specialized structure that regulates passage across blood and central nervous system (CNS) compartments. Despite its critical physiological role, there are no reliable in vitro models that can mimic hBBB development and function. Here, we constructed hBBB assembloids from brain and blood vessel organoids derived from human pluripotent stem cells. We validated the acquisition of blood-brain barrier (BBB)-specific molecular, cellular, transcriptomic, and functional characteristics and uncovered an extensive neuro-vascular crosstalk with a spatial pattern within hBBB assembloids. When we used patient-derived hBBB assembloids to model cerebral cavernous malformations (CCMs), we found that these assembloids recapitulated the cavernoma anatomy and BBB breakdown observed in patients. Upon comparison of phenotypes and transcriptome between patient-derived hBBB assembloids and primary human cavernoma tissues, we uncovered CCM-related molecular and cellular alterations. Taken together, we report hBBB assembloids that mimic the core properties of the hBBB and identify a potentially underlying cause of CCMs.

A 3D Microfluidic Device with Vertical Channels toward In Vitro Reconstruction of Blood-Brain Barrier.

This paper reports a three-dimensional microfluidic device with an array of vertical channels to enable regulated, continuous, vertical flows to emulate the environment for in vitro culturing of brain and blood vessel organoids. This is expected to ultimately lead to in vitro reconstruction of the blood-brain barrier that is of high interest to studies on mental illness mechanisms and drug delivery to the brain. Twelve vertical microfluidic channels, each with 300 µm diameter and 5 mm height, were formed in the high-permeability agar gel surrounding the organoid to realize the vertical circulation flows and to allow lateral diffusion flows. The combined vertical flow rate of all channels ranges from 2.1 to 6.8 mL/min under different control parameters. A 30-day-old human blood vessel organoid was planted into the device for initial culturing and flow function tests. The result indicates that the organoid was properly activated with effective flow generation in the culturing site of the device.

Short tandem repeats are important contributors to silencer elements in T cells.

The action of cis-regulatory elements with either activation or repression functions underpins the precise regulation of gene expression during normal development and cell differentiation. Gene activation by the combined activities of promoters and distal enhancers has been extensively studied in normal and pathological contexts. In sharp contrast, gene repression by cis-acting silencers, defined as genetic elements that negatively regulate gene transcription in a position-independent fashion, is less well understood. Here, we repurpose the STARR-seq approach as a novel high-throughput reporter strategy to quantitatively assess silencer activity in mammals. We assessed silencer activity from DNase hypersensitive I sites in a mouse T cell line. Identified silencers were associated with either repressive or active chromatin marks and enriched for binding motifs of known transcriptional repressors. CRISPR-mediated genomic deletions validated the repressive function of distinct silencers involved in the repression of non-T cell genes and genes regulated during T cell differentiation. Finally, we unravel an association of silencer activity with short tandem repeats, highlighting the role of repetitive elements in silencer activity. Our results provide a general strategy for genome-wide identification and characterization of silencer elements.

The effect of an artificial intelligence algorithm on chest X-ray interpretation of radiology residents.

OBJECTIVE: Chest X-rays are the most commonly performed diagnostic examinations. An artificial intelligence (AI) system that evaluates the images fast and accurately help reducing workflow and management of the patients. An automated assistant may reduce the time of interpretation in daily practice. We aim to investigate whether radiology residents consider the recommendations of an AI system for their final decisions, and to assess the diagnostic performances of the residents and the AI system. METHODS: Posteroanterior (PA) chest X-rays with confirmed diagnosis were evaluated by 10 radiology residents. After interpretation, the residents checked the evaluations of the AI Algorithm and made their final decisions. Diagnostic performances of the residents without AI and after checking the AI results were compared. RESULTS: Residents' diagnostic performance for all radiological findings had a mean sensitivity of 37.9% (vs 39.8% with AI support), a mean specificity of 93.9% (vs 93.9% with AI support). The residents obtained a mean AUC of 0.660 vs 0.669 with AI support. The AI algorithm diagnostic accuracy, measured by the overall mean AUC, was 0.789. No significant difference was detected between decisions taken with and without the support of AI. CONCLUSION: Although, the AI algorithm diagnostic accuracy were higher than the residents, the radiology residents did not change their final decisions after reviewing AI recommendations. In order to benefit from these tools, the recommendations of the AI system must be more precise to the user. ADVANCES IN KNOWLEDGE: This research provides information about the willingness or resistance of radiologists to work with AI technologies via diagnostic performance tests. It also shows the diagnostic performance of an existing AI algorithm, determined by real-life data.

Clinical Study of Mesenchymal Stem/Stromal Cell Therapy for the Treatment of Frailty: A Proposed Experimental Design for Therapeutic and Mechanistic Investigation.

Frailty, a specific condition of increased vulnerability and reduced general health associated with aging in older people, is an emerging problem worldwide with major implications for clinical practice and public health. Recent preclinical and clinical studies have supported the safety of mesenchymal stem/stromal cells (MSCs) in the treatment of frailty. Comprehensive study is needed to assess the interrelationship between the condition of frailty and the effects of MSC-based therapy. This randomized controlled phase I/II trial aims to investigate the safety and potential therapeutic efficacy of the allogeneic administration of umbilical cord-derived MSCs (UC-MSCs) in combination with the standard treatment for frailty in Vietnam. Moreover, this study describes the rationales, study designs, methodologies, and analytical strategies currently employed in stem cell research and clinical studies. The primary outcome measures will include the incidences of prespecified administration-associated adverse events and serious adverse events. The potential efficacy will be evaluated based on improvements in frailty conditions (including those determined through a physical examination, patient-reported outcomes, quality of life, immune markers of frailty, metabolism analysis, and cytokine markers from patient plasma). This clinical trial and stem cell analysis associated with patient sampling at different time points aim to identify and characterize the potential effects of UC-MSCs on improving frailty based on the stem cell quality, cytokine/growth factor secretion profiles of UC-MSCs, cellular senescence, and metabolic analysis of patient CD3+ cells providing fundamental knowledge for designing and implementing research strategies in future studies. Clinical Trials Registration Number: NCT04919135.

Novel findings from family-based exome sequencing for children with biliary atresia.

Biliary atresia (BA) is a progressive inflammation and fibrosis of the biliary tree characterized by the obstruction of bile flow, which results in liver failure, scarring and cirrhosis. This study aimed to explore the elusive aetiology of BA by conducting whole exome sequencing for 41 children with BA and their parents (35 trios, including 1 family with 2 BA-diagnosed children and 5 child-mother cases). We exclusively identified and validated a total of 28 variants (17 X-linked, 6 de novo and 5 homozygous) in 25 candidate genes from our BA cohort. These variants were among the 10% most deleterious and had a low minor allele frequency against the employed databases: Kinh Vietnamese (KHV), GnomAD and 1000 Genome Project. Interestingly, AMER1, INVS and OCRL variants were found in unrelated probands and were first reported in a BA cohort. Liver specimens and blood samples showed identical variants, suggesting that somatic variants were unlikely to occur during morphogenesis. Consistent with earlier attempts, this study implicated genetic heterogeneity and non-Mendelian inheritance of BA.

Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.

Gene expression is controlled by the involvement of gene-proximal (promoters) and distal (enhancers) regulatory elements. Our previous results demonstrated that a subset of gene promoters, termed Epromoters, work as bona fide enhancers and regulate distal gene expression. Here, we hypothesized that Epromoters play a key role in the coordination of rapid gene induction during the inflammatory response. Using a high-throughput reporter assay we explored the function of Epromoters in response to type I interferon. We find that clusters of IFNa-induced genes are frequently associated with Epromoters and that these regulatory elements preferentially recruit the STAT1/2 and IRF transcription factors and distally regulate the activation of interferon-response genes. Consistently, we identified and validated the involvement of Epromoter-containing clusters in the regulation of LPS-stimulated macrophages. Our findings suggest that Epromoters function as a local hub recruiting the key TFs required for coordinated regulation of gene clusters during the inflammatory response.

Preservation of grape tomato by isochoric freezing.

This study investigated the potential of isochoric freezing to preserve tomatoes. Isochoric freezing is an emerging technology that preserves biological matter at subfreezing temperatures without any ice damage. Isochoric freezing was compared with freezing under isobaric conditions and with preservation techniques used in the food industry: cold storage at 10 °C and individual quick freezing (IQF). Physicochemical and nutritional properties were evaluated weekly for four weeks. Preservation under isochoric conditions maintained the mass, color, nutrient content (ascorbic acid, lycopene and phenolics) and antioxidant activity of the fresh tomatoes. Also, isochoric preservation led to minimal texture damage. In comparison, mass loss of tomatoes stored at 10 °C for 3 weeks contributed to changes in overall visual quality and firmness as well as significant losses in nutrient content. The greatest mass, texture, and nutrients losses were obtained for tomatoes subjected to IQF and isobaric freezing. The results show that isochoric freezing has the potential to preserve tomatoes while maintaining physicochemical and nutritional properties similar to those of fresh tomatoes which might find application in the commercial preservation of tomatoes.

Predicting COVID-19 Pneumonia Severity on Chest X-ray With Deep Learning.

Introduction The need to streamline patient management for coronavirus disease-19 (COVID-19) has become more pressing than ever. Chest X-rays (CXRs) provide a non-invasive (potentially bedside) tool to monitor the progression of the disease. In this study, we present a severity score prediction model for COVID-19 pneumonia for frontal chest X-ray images. Such a tool can gauge the severity of COVID-19 lung infections (and pneumonia in general) that can be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. Methods Images from a public COVID-19 database were scored retrospectively by three blinded experts in terms of the extent of lung involvement as well as the degree of opacity. A neural network model that was pre-trained on large (non-COVID-19) chest X-ray datasets is used to construct features for COVID-19 images which are predictive for our task. Results This study finds that training a regression model on a subset of the outputs from this pre-trained chest X-ray model predicts our geographic extent score (range 0-8) with 1.14 mean absolute error (MAE) and our lung opacity score (range 0-6) with 0.78 MAE. Conclusions These results indicate that our model's ability to gauge the severity of COVID-19 lung infections could be used for escalation or de-escalation of care as well as monitoring treatment efficacy, especially in the ICU. To enable follow up work, we make our code, labels, and data available online.

Analysis of Allergan's Biocell Implant Recall in a Major University Breast Center.

BACKGROUND: In May 2019, Health Canada released a national recall of all macrotextured breast implants that later became international in July 2019 regarding increasing accounts of suspected breast implant-associated anaplastic large cell lymphoma. In Canada, this recall targeted Allergan's Biocell implants. This report presents the postmortem of this comprehensive single-center recall, which had to be undertaken in a limited time. METHODS: Four months after the beginning of the recall, the authors analyzed the transcript of meetings to characterize the team assembled during the recall. Then, to reconstruct the systemic work plan as well as the crucial steps and actors of the recall process, a chronologic table of the 5 meetings held during the recall, agendas and transcripts of every meeting, electronic correspondences, and other documents created during the recall were consulted. RESULTS: Between 1996 and 2018, 1260 women were affected by the recall, meaning that they received Allergan's macrotextured implants. Ninety-two patients underwent explantation of the device or will undergo implant explantation. To this day, no patient was diagnosed with breast implant-associated anaplastic large cell lymphoma. CONCLUSIONS: Our center's experience highlights the utmost importance of building a national breast implants registry. We recommend breast centers to develop preestablished crisis centers and train staff to better prepare for future device recalls and minimize waste of time. Finally, we believe that implants should be identified based on the characteristics rather than their brand name.

Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation.

During thymic development and upon peripheral activation, T cells undergo extensive phenotypic and functional changes coordinated by lineage-specific developmental programs. To characterize the regulatory landscape controlling T cell identity, we perform a wide epigenomic and transcriptional analysis of mouse thymocytes and naive CD4 differentiated T helper cells. Our investigations reveal a dynamic putative enhancer landscape, and we could validate many of the enhancers using the high-throughput CapStarr sequencing (CapStarr-seq) approach. We find that genes using multiple promoters display increased enhancer usage, suggesting that apparent "enhancer redundancy" might relate to isoform selection. Furthermore, we can show that two Runx3 promoters display long-range interactions with specific enhancers. Finally, our analyses suggest a novel function for the PRC2 complex in the control of alternative promoter usage. Altogether, our study has allowed for the mapping of an exhaustive set of active enhancers and provides new insights into their function and that of PRC2 in controlling promoter choice during T cell differentiation.

Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene.

The Ikzf1 locus encodes the lymphoid specific transcription factor Ikaros, which plays an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus.

Genetic landscape of autism spectrum disorder in Vietnamese children.

Autism spectrum disorder (ASD) is a complex disorder with an unclear aetiology and an estimated global prevalence of 1%. However, studies of ASD in the Vietnamese population are limited. Here, we first conducted whole exome sequencing (WES) of 100 children with ASD and their unaffected parents. Our stringent analysis pipeline was able to detect 18 unique variants (8 de novo and 10 ×-linked, all validated), including 12 newly discovered variants. Interestingly, a notable number of X-linked variants were detected (56%), and all of them were found in affected males but not in affected females. We uncovered 17 genes from our ASD cohort in which CHD8, DYRK1A, GRIN2B, SCN2A, OFD1 and MDB5 have been previously identified as ASD risk genes, suggesting the universal aetiology of ASD for these genes. In addition, we identified six genes that have not been previously reported in any autism database: CHM, ENPP1, IGF1, LAS1L, SYP and TBX22. Gene ontology and phenotype-genotype analysis suggested that variants in IGF1, SYP and LAS1L could plausibly confer risk for ASD. Taken together, this study adds to the genetic heterogeneity of ASD and is the first report elucidating the genetic landscape of ASD in Vietnamese children.

Preliminary Results Supporting the Bacterial Hypothesis in Red Breast Syndrome following Postmastectomy Acellular Dermal Matrix- and Implant-Based Reconstructions.

Acellular dermal matrices have become a mandatory tool in reconstructive breast surgery. Since their introduction, they have been considered to be nonreactive and nonimmunogenic scaffolds. However, some patients who undergo implant-based breast reconstruction with acellular dermal matrices develop postoperative cutaneous erythema overlying their matrices, a condition commonly referred to as red breast syndrome. The aim of this study was to gain a better understanding of this phenomenon. An analysis was conducted on consecutive patients who underwent acellular dermal matrix- and implant-based breast reconstructions and developed red breast syndrome that was treated surgically between April of 2017 and June of 2018 at the authors' institution. During surgery, 1-cm specimens of acellular dermal matrix were sampled and analyzed by scanning electron microscopy. Observations were charted to score and record the presence and thickness of biofilm, and for identification of bacteria. These measurements were performed using Adobe Photoshop CS6 Extended software. Six postmastectomy breast reconstruction patients were included, all with AlloDerm Ready-to-Use-based reconstructions. All specimens were colonized by various bacteria ranging from Gram-negative bacilli to Gram-positive microorganisms. Biofilm was present in all studied specimens. The cause of skin erythema overlying acellular dermal matrix grafts, and the so-called red breast syndrome, may be related to contamination with various bacteria. Although contamination was omnipresent in analyzed samples, its clinical significance is variable. Even if acellular dermal matrix-based reconstructions are salvaged, this could come at the price of chronic local inflammation.

A Vietnamese human genetic variation database.

Large scale human genome projects have created tremendous human genome databases for some well-studied populations. Vietnam has about 95 million people (the 14th largest country by population in the world) of which more than 86% are Kinh people. To date, genetic studies for Vietnamese people mostly rely on genetic information from other populations. Building a Vietnamese human genetic variation database is a must for properly interpreting Vietnamese genetic variants. To this end, we sequenced 105 whole genomes and 200 whole exomes of 305 unrelated Kinh Vietnamese (KHV) people. We also included 101 other previously published KHV genomes to build a Vietnamese human genetic variation database of 406 KHV people. The KHV database contains 24.81 million variants (22.47 million single nucleotide polymorphisms (SNPs) and 2.34 million indels) of which 0.71 million variants are novel. It includes more than 99.3% of variants with a frequency of >1% in the KHV population. Noticeably, the KHV database revealed 107 variants reported in the human genome mutation database as pathological mutations with a frequency above 1% in the KHV population. The KHV database (available at https://genomes.vn) would be beneficial for genetic studies and medical applications not only for the Vietnamese population but also for other closely related populations.

In-situ characterization of the bacterial biofilm associated with Xeroform™ and Kaltostat™ dressings and evaluation of their effectiveness on thin skin engraftment donor sites in burn patients.

Biofilm forms when bacteria surrounded by an extracellular matrix aggregate on a surface. It can develop on many surfaces, including wound dressings; this can be particularly nefarious for burn patients undergoing skin grafting (autograft) for burn wound coverage as they often suffer from compromised immune system function. Autograft donor sites are particularly vulnerable to biofilm formation; as such, timely healing of these sites is essential. Our aim was to apply scanning electron microscopy to compare the efficacy of two types of wound dressings in preventing the formation of bacterial biofilm on burn patient skin graft donor sites. One dressing contained bismuth tribromophenate at a concentration of 3% which confers it bacteriostatic properties (Xeroform™). The other was an absorptive alginate calcium sodium dressing (Kaltostat™). Samples of each wound dressing, which were in contact with the skin graft donor site, were prepared for analysis under the scanning electron microscope (SEM) using an original method developed by our research group that aims to maintain the integrity of the biofilm microstructure. Samples prepared by this method were then analyzed using SEM, which allowed the characterization of biofilm and the evaluation of bacterial density on the studied dressing samples. To this day, this imaging technique has been rarely employed for dressing analysis and this is the first time that it is employed for in situ biofilm visualization for this particular application.

A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation.

Normal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models. Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8- double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation. Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Cas9-mediated genetic deletion of Robnr, an inducible lncRNA located downstream of the anti-apoptotic gene Bcl2, demonstrated a critical role of the Robnr locus in the induction of Bcl2. Thus, the pro-T-cell line P5424 is a powerful model system to characterize regulatory networks involved in early T-cell differentiation and maturation.