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• Integrated Epigenetic Maps of Human Embryonic, Extraembryonic and Adult Cells

  Working cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) funded by this Roadmap mechanism we have comprehensively mapped the epigenomes of select human cells with significant relevance to complex human disease. Our effort has been focused on cells relevant to human health and complex disease including cells from the blood, brain, breast, skin, male germ cells, extraembryonic tissues and trophoblast, and U.S. Government-approved lines of human embryonic stem cells. We have incorporated high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. The resulting comprehensive maps include up to 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin (H3K4me1, H3K4me3, H3K9me3, H3K9ac, H3K27ac, H3K27me3, H3K36me3), DNA methylation, miRNA and gene expression, and for select cases whole genome shotgun sequence. Our cell and data production pipeline incorporates verification and data validation with independent methods, and operates under a model motivated by increased data production and decrease cost. Our group in conjunction with the other REMC teams, the EDACC, ENCODE, Epigenetics of Human Health and Disease centers and the NIH Roadmap program are developing methods, tools and reference epigenome maps for the research community that will make the promise of epigenetics in understand and treating human complex disease a reality. Our reference epigenomes will enable new disciplines including human population epigenetics, comparative epigenomics, neuroepigenetics, and therapeutic epigenetics for tissue regeneration and reversal of disease.

  Study phs000791

• Biopsy-Derived Organoids in Personalised Early Breast Cancer Care: Challenges of Tumour Purity and Normal Cell Overgrowth Cap Their Practical Utility

  The ability to establish organoids composed exclusively of tumour rather than healthy cells is essential for their implementation into clinical practice. Organoids have in recent years emerged as a powerful tool to expand patient material in culture and generate modifiable 3D models derived from humans or animal models. For translational research, they enable the creation of model systems for an ever-increasing number of cell types and diseases. And in personalised medicine, they potentially allow for functional drug testing with high predictive power in certain settings. We found that using biopsy material from untreated, early-stage primary breast cancer patients poses significant challenges for consistently culturing tumour cells as organoids. Specifically, we observed frequent outgrowth of genetically normal, non-cancerous epithelial cells. We analysed >100 biopsy samples from early-stage breast cancer and present our large collection of >70 organoid lines. We also show methods of assessing successful tumour cell culture in a time and cost-efficient manner, proving a high rate (>85%) of normal cell overgrowth in early-stage breast cancer organoids. Finally, we show a number of successful attempts to culture cancer organoids from mastectomy-derived tissue of advanced, metastatic breast cancer. We conclude that the usefulness of organoids from early breast cancer for translational research and personalised medicine, especially guidance of adjuvant or post-surgical maintenance therapy, is strongly limited by the low success rate of culturing cancerous cells under organoid conditions.

  Study EGAS50000000605

• Massively parallel nanowell-based single-cell gene expression profiling

  Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample. The system employs a 5184-nanowell-containing microchip to capture ~1300 single cells and process them. Each nanowell contains preprinted oligonucleotides encoding poly-d(T), a unique well barcode, and a unique molecular identifier. The ICELL8 system uses imaging software to identify nanowells containing viable single cells and only wells with single cells are processed into sequencing libraries. Here, we report the performance and utility of ICELL8 using samples of increasing complexity from cultured cells to mouse solid tissue samples. Our assessment of the system to discriminate between mixed human and mouse cells showed that ICELL8 has a low cell multiplet rate (< 3%) and low cross-cell contamination. We characterized single-cell transcriptomes of more than a thousand cultured human and mouse cells as well as 468 mouse pancreatic islets cells. We were able to identify distinct cell types in pancreatic islets, including alpha, beta, delta and gamma cells. Overall, ICELL8 provides efficient and cost-effective single-cell expression profiling of thousands of cells, allowing researchers to decipher single-cell transcriptomes within complex biological samples.

  Study EGAS00001002320

• Exploiting evolutionary steering in cancer therapy

  Drug resistance, mediated by intra-tumour heterogeneity and clonal evolution, is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at the cost of increased sensitivity to another due to so-called evolutionary trade-offs. This weakness can be exploited in the clinic using an approach called ‘evolutionary herding’ that aims at controlling the tumour cell population to delay or prevent resistance. However, model systems able to recapitulate cancer evolution experimentally are lacking and current in vitro techniques based on small populations, re-plating and escalating dose, are unsuitable to develop evolutionary herding strategies. We present a novel methodology for evolutionary herding in vitro and ex vivo using patient-derived organoids. Our approach is based on a combination of single-cell barcoding, very large populations of 108-109 cells grown without re-plating, realistic high drug doses, time-course monitoring of cancer clones, and mathematical modelling of tumour evolutionary dynamics. We demonstrate evolutionary herding in non-small cell lung cancer in vitro and in patient-derived colorectal cancer organoids (PDO). We show that herding causes controlled evolutionary bottlenecks that lead to collateral sensitivity. Through genomic analysis, we were also able to determine the mechanisms that drive such sensitivity. Our approach allows modelling evolutionary trade-offs experimentally to test patient-specific evolutionary herding strategies that can be translated into the clinic to control treatment resistance.

  Study EGAS00001003200

• Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

  Background The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulfite-based cfDNA methylation profiling. Methods 15 tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulfite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. Results All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. Conclusion The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.

  Study EGAS00001004271

• Combining transcription factor binding affinities with open chromatin data for accurate gene expression prediction

  The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid cost and labour intensive TF ChIP-seq assays.It is important to develop reliable and fast computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices.TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq, using either peaks or footprints as input.In addition to open-chromatin data, also Histone-Marks (HMs) can be used in TEPIC to identify candidate TF binding sites.TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength.Using machine learning techniques, we show that incorporating low affinity binding sites improves our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites.Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance.In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq datasets.Finally, we show that these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively.

  Study EGAS00001002073

• A Retrospective and Cross-Sectional Analysis of Patients Treated for SCID Since January 1, 1968

  Individuals with a past diagnosis of severe combined immune deficiency (including many cases of "leaky SCID", Omenn syndrome, and reticular dysgenesis) who have undergone blood and marrow transplant, gene therapy, or enzyme replacement in the past may be eligible for 6902. The purpose of 6902 is very similar to 6901, except 6902 is looking backwards at what has already been done in the past (compared to 6901 which is looking into the future). Over 800 patients with SCID are expected to be enrolled on 6902. This makes 6902 the largest study ever to describe outcomes for patients with SCID treated at many different hospitals around North America. One of the most important components of the 6902 study is the "cross sectional" study. Patients who have received their treatments (BMT, gene therapy, enzyme replacement) many years ago are asked to come back to the hospital where they were treated. During this visit, additional research blood work is drawn and information is gathered regarding long-term transplant outcomes such as infections, graft-versus-host disease, autoimmune diseases, and quality of life. This will allow PIDTC researchers to better understand long-term outcomes from procedures that occurred many years ago (sometimes over 30 years ago) - something that is not possible at the present time with 6901. This will help researchers to best design new treatments and clinical trials in the future for children with SCID.

  Study phs001326

• QUANTitative Chest Computed Tomography UnMasking Emphysema Progression in Alpha-1 Antitrypsin Deficiency

  AAT deficiency is a genetic disorder associated with emphysema. Spirometry, the lung function test that measures how well the lungs exhale air, is used to diagnose and track the progression of emphysema. Some studies have suggested that forced expiratory volume in 1 second (FEV1) measurements, a type of spirometry test, may lack accuracy in detecting disease progression in cases of severe AAT deficiency. Another method, high resolution chest CT scans, may be more accurate at measuring the progression of emphysema. The purpose of this study is to determine if high resolution CT scans are better at detecting the progression of emphysema than lung function tests. Results from this study may lead to the development of a more accurate way to assess lung tissue loss and may improve the understanding of lung destruction in AAT deficiency. This study will last 4 years and will enroll people with AAT deficiency who have nearly normal lung function test results. Study visits, each lasting about 4 hours, will occur at baseline and months 6, 12, 18, 24, and 36. At each visit, participants will undergo lung function tests, a CT scan, blood collection, and a physical exam. Female participants will have urine collected for a pregnancy test. All participants will also complete questionnaires to assess health status and lung function. Study researchers will call participants every 2 months to collect information on lung disease symptoms and medication changes.

  Study phs000698

• Experimental PfSPZ Vaccine in Adults Without Malaria

  The study was performed to evaluate whole-blood transcriptomic profiles via RNA-seq before, during, and after immunization with the PfSPZ Vaccine in malaria-naïve, healthy adults enrolled in VRC 312 (NCT01441167). VRC 312 was the second study of the PfSPZ Vaccine and the first study to evaluate intravenous (IV) administration of this vaccine. The study was an open-label evaluation of the safety, tolerability, immunogenicity, and protective efficacy of the vaccine at successively higher administered by the IV route. The highest dosages were evaluated for protection against a malaria challenge after 4 to 6 vaccinations. The primary objectives of the study were related to the safety and tolerability of the vaccine at the 4 different dosage levels when administered IV; the secondary objectives were related to PfSPZ vaccine-mediated protection against Plasmodium falciparum (Pf) challenge at the 3 higher dosage levels, and the exploratory objectives were related to the immunogenicity of the PfSPZ Vaccine and defining an immune correlate of protection. To further determine potential molecular correlates of immunogenicity and/or protection, RNA-seq was performed on whole blood collected from subjects in all dose groups at time points before, during, and after immunization.

  Study phs002422

• Gut microbiome dynamics unravelled with metagenomics sequencing

  It has been already several years since we discovered that microbial therapeutics like Faecal Microbiota Transplantation can be used to treat Clostridium difficile infection (CDI) and Inflammatory bowel disease (IBD) with great success. The concept has challenged us to test the limits of our knowledge with the perspective to improve health in the most diverse conditions like Parkinson disease, depression, autism and obesity, just to mention a few. Note: the figure belongs to the original paper and is owned by the authors. Allyson L.Bird and colleagues from Genentech Inc. (San Francisco) recently published an interesting study building up on the key concept that “As microbial therapeutics are increasingly being tested in diverse patient populations, it is essential to understand the host and environmental factors influencing the microbiome.” The authors of this work analysed 1359 gut microbiome samples using shotgun metagenomics sequencing.  The results of the comparison done between microbiota composition across the different groups showed that biological sex is the strongest driver of diversity, while aging (age range studied: 20–69) appears to be the second factor. As smartly outlined in the authors’ own graphical abstract (figure to the left), Bacteroidota species consistently increased with donors' age while Actinobacteriota species, including Bifidobacterium, decreased. This study also integrated data from oncological patients to draw cancer-related evidences. After correcting the biases for technical and geographic differences, they found that cancer patients show significantly altered gut bacterial communities compared with their healthy counterparts. Eg. E.coli was found to be increased in cancer patients together with Bacteroidota/Firmicutes ratios. By comparing sequential samples taken from the same donors (413) within short-distance time points, the authors found that in the short term, intra-individual differences were less than the inter-individual ones, indicating a certain community stability being the norm. One of the pivotal points from this interesting study is that the data proceeds from extremely well-defined and selected donors. Specifically, the data for 949 selected healthy donors came from the Milieu Intérieur (MI) Consortium and extensive metadata, including demographic variables, serological measures, dietary information, and systemic immune profiles, are available. This precise stratification allowed for the robust detection of smaller changes, compared to former works. All sequencing data has been deposited in the EGA archive under the accession number EGAS00001004437. Enjoy this amazing open access paper published in the Experimental Journal of Medicine on January 2021.

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