Using patient-derived tumor organoids from common epithelial cancers to analyze personalized T-cell responses to neoantigens.

Adoptive cell transfer of tumor-infiltrating lymphocytes (TIL) can mediate durable complete responses in some patients with common epithelial cancers but does so infrequently. A better understanding of T-cell responses to neoantigens and tumor-related immune evasion mechanisms requires having the autologous tumor as a reagent. We investigated the ability of patient-derived tumor organoids (PDTO) to fulfill this need and evaluated their utility as a tool for selecting T-cells for adoptive cell therapy. PDTO established from metastases from patients with colorectal, breast, pancreatic, bile duct, esophageal, lung, and kidney cancers underwent whole exomic sequencing (WES), to define mutations. Organoids were then evaluated for recognition by autologous TIL or T-cells transduced with cloned T-cell receptors recognizing defined neoantigens. PDTO were also used to identify and clone TCRs from TIL targeting private neoantigens and define those tumor-specific targets. PDTO were successfully established in 38/47 attempts. 75% were available within 2 months, a timeframe compatible with screening TIL for clinical administration. These lines exhibited good genetic fidelity with their parental tumors, especially for mutations with higher clonality. Immunologic recognition assays demonstrated instances of HLA allelic loss not found by pan-HLA immunohistochemistry and in some cases WES of fresh tumor. PDTO could also be used to show differences between TCRs recognizing the same antigen and to find and clone TCRs recognizing private neoantigens. PDTO can detect tumor-specific defects blocking T-cell recognition and may have a role as a selection tool for TCRs and TIL used in adoptive cell therapy.

scOrange-a tool for hands-on training of concepts from single-cell data analytics.

MOTIVATION: Single-cell RNA sequencing allows us to simultaneously profile the transcriptomes of thousands of cells and to indulge in exploring cell diversity, development and discovery of new molecular mechanisms. Analysis of scRNA data involves a combination of non-trivial steps from statistics, data visualization, bioinformatics and machine learning. Training molecular biologists in single-cell data analysis and empowering them to review and analyze their data can be challenging, both because of the complexity of the methods and the steep learning curve. RESULTS: We propose a workshop-style training in single-cell data analytics that relies on an explorative data analysis toolbox and a hands-on teaching style. The training relies on scOrange, a newly developed extension of a data mining framework that features workflow design through visual programming and interactive visualizations. Workshops with scOrange can proceed much faster than similar training methods that rely on computer programming and analysis through scripting in R or Python, allowing the trainer to cover more ground in the same time-frame. We here review the design principles of the scOrange toolbox that support such workshops and propose a syllabus for the course. We also provide examples of data analysis workflows that instructors can use during the training. AVAILABILITY AND IMPLEMENTATION: scOrange is an open-source software. The software, documentation and an emerging set of educational videos are available at http://singlecell.biolab.si.

A multicenter study of 30 days complications after deceased donor liver transplantation in the model for end-stage liver disease score era.

Knowledge of risk factors for posttransplant complications is likely to improve patient outcomes. Few large studies of all early postoperative complications after deceased donor liver transplantation (DDLT) exist. Therefore, we conducted a retrospective, cohort study of 30-day complications, their risk factors, and the impact on outcomes after DDLT. Three centers contributed data for 450 DDLTs performed from January 2005 through December 2009. Data included donor, recipient, transplant, and outcome variables. All 30-day postoperative complications were graded by the Clavien-Dindo system. Complications per patient and severe (≥ grade III) complications were primary outcomes. Death within 30 days, complication occurrence, length of stay (LOS), and graft and patient survival were secondary outcomes. Multivariate associations of risk factors with complications and complications with LOS, graft survival, and patient survival were examined. Mean number of complications/patient was 3.3 ± 3.9. At least 1 complication occurred in 79.3%, and severe complications occurred in 62.8% of recipients. Mean LOS was 16.2 ± 22.9 days. Graft and patient survival rates were 84% and 86%, respectively, at 1 year and 74% and 76%, respectively, at 3 years. Hospitalization, critical care, ventilatory support, and renal replacement therapy before transplant and transfusions during transplant were the significant predictors of complications (not the Model for End-Stage Liver Disease score). Both number and severity of complications had a significant impact on LOS and graft and patient survival. Structured reporting of risk-adjusted complications rates after DDLT is likely to improve patient care and transplant center benchmarking. Despite the accomplished reductions in transfusions during DDLT, opportunities exist for further reductions. With increasing transplantation of sicker patients, reduction in complications would require multidisciplinary efforts and institutional commitment. Pretransplant risk characteristics for complications must factor in during payer contracting.

Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae.

Cooperation is central to many major transitions in evolution, including the emergence of eukaryotic cells, multicellularity and eusociality. Cooperation can be destroyed by the spread of cheater mutants that do not cooperate but gain the benefits of cooperation from others. However, cooperation can be preserved if cheaters are facultative, cheating others but cooperating among themselves. Several cheater mutants have been studied before, but no study has attempted a genome-scale investigation of the genetic opportunities for cheating. Here we describe such a screen in a social amoeba and show that cheating is multifaceted by revealing cheater mutations in well over 100 genes of diverse types. Many of these mutants cheat facultatively, producing more than their fair share of spores in chimaeras, but cooperating normally when clonal. These findings indicate that phenotypically stable cooperative systems may nevertheless harbour genetic conflicts. The opportunities for evolutionary moves and countermoves in such conflicts may select for the involvement of multiple pathways and numerous genes.

Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex.

Colorectal cancers (CRCs) are prevalent worldwide, yet current treatments remain inadequate. Using chemical genetic screens, we identify that co-inhibition of topoisomerase I (TOP1) and NEDD8 is synergistically cytotoxic in human CRC cells. Combination of the TOP1 inhibitor irinotecan or its bioactive metabolite SN38 with the NEDD8-activating enzyme inhibitor pevonedistat exhibits synergy in CRC patient-derived organoids and xenografts. Mechanistically, we show that pevonedistat blocks the ubiquitin/proteasome-dependent repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors and that the CUL4-RBX1 complex (CRL4) is a prominent ubiquitin ligase acting on TOP1-DPCs for proteasomal degradation upon auto-NEDD8 modification during replication. We identify DCAF13, a DDB1 and Cullin Associated Factor, as the receptor of TOP1-DPCs for CRL4. Our study not only uncovers a replication-coupled ubiquitin-proteasome pathway for the repair of TOP1-DPCs but also provides molecular and translational rationale for combining TOP1 inhibitors and pevonedistat for CRC and other types of cancers.

Breast Cancers Are Immunogenic: Immunologic Analyses and a Phase II Pilot Clinical Trial Using Mutation-Reactive Autologous Lymphocytes.

PURPOSE: Metastatic breast cancer (mBrCa) is most often an incurable disease with only modest responses to available immunotherapies. This study investigates the immunogenicity of somatic mutations in breast cancer and explores the therapeutic efficacy in a pilot trial of mutation-reactive tumor-infiltrating lymphocytes (TILs) in patients with metastatic disease. PATIENTS AND METHODS: Forty-two patients with mBrCa refractory to previous lines of treatment underwent surgical resection of a metastatic lesion(s), isolation of TIL cultures, identification of exomic nonsynonymous tumor mutations, and immunologic screening for neoantigen reactivity. Clinically eligible patients with appropriate reactivity were enrolled into one cohort of an ongoing phase II pilot trial of adoptive cell transfer of selected neoantigen-reactive TIL, with a short course of pembrolizumab (ClinicalTrials.gov identifier: NCT01174121). RESULTS: TILs were isolated and grown in culture from the resected lesions of all 42 patients with mBrCa, and a median number of 112 (range: 6-563) nonsynonymous mutations per patient were identified. Twenty-eight of 42 (67%) patients contained TIL that recognized at least one immunogenic somatic mutation (median: 3 neoantigens per patient, range: 1-11), and 13 patients demonstrated robust reactivity appropriate for adoptive transfer. Eight patients remained clinically eligible for treatment, and six patients were enrolled on a protocol of adoptive cell transfer of enriched neoantigen-specific TIL, in combination with pembrolizumab (≤ 4 doses). Objective tumor regression was noted in three patients, including one complete response (now ongoing over 5.5 years) and two partial responses (6 and 10 months). CONCLUSION: Most patients with breast cancer generated a natural immune response targeting the expressed products of their cancer mutations. Adoptive transfer of TIL is a highly personalized experimental option for patients with mBrCa shown to be capable of mediating objective responses in this pilot trial and deserves further study.

Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers.

The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen-specific TCR clonotypes (NeoTCRs) from 10 metastatic human tumors to their single-cell transcriptomes, we identified signatures of CD8+ and CD4+ neoantigen-reactive tumor-infiltrating lymphocytes (TILs). Neoantigen-specific TILs exhibited tumor-specific expansion with dysfunctional phenotypes, distinct from blood-emigrant bystanders and regulatory TILs. Prospective prediction and testing of 73 NeoTCR signature-derived clonotypes demonstrated that half of the tested TCRs recognized tumor antigens or autologous tumors. NeoTCR signatures identified TCRs that target driver neoantigens and nonmutated viral or tumor-associated antigens, suggesting a common metastatic TIL exhaustion program. NeoTCR signatures delineate the landscape of TILs across metastatic tumors, enabling successful TCR prediction based purely on TIL transcriptomic states for use in cancer immunotherapy.

Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor-Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors.

Adoptive cellular therapy (ACT) targeting neoantigens can achieve durable clinical responses in patients with cancer. Most neoantigens arise from patient-specific mutations, requiring highly individualized treatments. To broaden the applicability of ACT targeting neoantigens, we focused on TP53 mutations commonly shared across different cancer types. We performed whole-exome sequencing on 163 patients with metastatic solid cancers, identified 78 who had TP53 missense mutations, and through immunologic screening, identified 21 unique T-cell reactivities. Here, we report a library of 39 T-cell receptors (TCR) targeting TP53 mutations shared among 7.3% of patients with solid tumors. These TCRs recognized tumor cells in a TP53 mutation- and human leucocyte antigen (HLA)-specific manner in vitro and in vivo. Twelve patients with chemorefractory epithelial cancers were treated with ex vivo-expanded autologous tumor-infiltrating lymphocytes (TIL) that were naturally reactive against TP53 mutations. However, limited clinical responses (2 partial responses among 12 patients) were seen. These infusions contained low frequencies of mutant p53-reactive TILs that had exhausted phenotypes and showed poor persistence. We also treated one patient who had chemorefractory breast cancer with ACT comprising autologous peripheral blood lymphocytes transduced with an allogeneic HLA-A*02-restricted TCR specific for p53R175H. The infused cells exhibited an improved immunophenotype and prolonged persistence compared with TIL ACT and the patient experienced an objective tumor regression (-55%) that lasted 6 months. Collectively, these proof-of-concept data suggest that the library of TCRs targeting shared p53 neoantigens should be further evaluated for the treatment of patients with advanced human cancers. See related Spotlight by Klebanoff, p. 919.

New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data.

BACKGROUND: Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential. RESULTS: Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of Dictyostelium discoideum development. The PKA network is well studied in D. discoideum but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in D. discoideum, and a histidine kinase, a candidate upstream regulator of PKA activity. CONCLUSIONS: The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.

mRNA vaccine-induced neoantigen-specific T cell immunity in patients with gastrointestinal cancer.

BACKGROUNDTherapeutic vaccinations against cancer have mainly targeted differentiation antigens, cancer-testis antigens, and overexpressed antigens and have thus far resulted in little clinical benefit. Studies conducted by multiple groups have demonstrated that T cells recognizing neoantigens are present in most cancers and offer a specific and highly immunogenic target for personalized vaccination.METHODSWe recently developed a process using tumor-infiltrating lymphocytes to identify the specific immunogenic mutations expressed in patients' tumors. Here, validated, defined neoantigens, predicted neoepitopes, and mutations of driver genes were concatenated into a single mRNA construct to vaccinate patients with metastatic gastrointestinal cancer.RESULTSThe vaccine was safe and elicited mutation-specific T cell responses against predicted neoepitopes not detected before vaccination. Furthermore, we were able to isolate and verify T cell receptors targeting KRASG12D mutation. We observed no objective clinical responses in the 4 patients treated in this trial.CONCLUSIONThis vaccine was safe, and potential future combination of such vaccines with checkpoint inhibitors or adoptive T cell therapy should be evaluated for possible clinical benefit in patients with common epithelial cancers.TRIAL REGISTRATIONPhase I/II protocol (NCT03480152) was approved by the IRB committee of the NIH and the FDA.FUNDINGCenter for Clinical Research, NCI, NIH.

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.

BACKGROUND: Bioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability. RESULTS: We have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment. CONCLUSION: dictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.

Systemic non-Hodgkin's lymphoma simulating primary intraocular lymphoma.

PURPOSE: To describe a case of an unusual presentation of systemic non-Hodgkin's lymphoma with clinical and histopathologic findings closely resembling that of primary intraocular lymphoma. DESIGN: Observational case report. METHODS: A 58-year-old woman with a history of treated systemic non-Hodgkin's lymphoma presented 2 years later with a subretinal lesion and intraocular inflammation in her left eye. RESULTS: Diagnostic enucleation and histopathologic studies revealed findings consistent with primary intraocular lymphoma including intraretinal, subretinal, and subretinal pigment epithelial tumor cells without involvement of the choroid. CONCLUSIONS: We conclude that systemic non-Hodgkin's lymphoma can present remotely with findings resembling primary intraocular lymphoma and should be included in the differential diagnosis of intraocular inflammation and subretinal infiltrates.

Correlation of MR perfusion imaging and vessel tortuosity parameters in assessment of intracranial neoplasms.

Advances in noninvasive imaging techniques such as magnetic resonance perfusion imaging have been found useful in grading cerebral neoplasms and have potential for significant clinical benefit. The purpose of this study was to determine the correlation between tumor vessel tortuosity as measured from vessels extracted from magnetic resonance angiograms (MRA) and perfusion parameters of cerebral blood flow (CBF) and cerebral blood volume (CBV) in intracranial neoplasms. We hypothesized that tumor blood vessel tortuosity measures and perfusion measures would be correlated, since both are increased by tumor angiogenesis. 18 patients with 19 cerebral neoplasms were evaluated with conventional MR imaging and dynamic contrast-enhanced T2-weighted perfusion MR imaging (PWI). Both benign and malignant lesions were included, as were hyper- and hypovascular tumors. Regions of interest were plotted within the tumor area to locate foci of maximum CBV and CBF. CBV and CBF measurements were also recorded in contralateral normal appearing white matter to calculate relative CBV (rCBV) and relative CBF (rCBF). Vessel tortuosity analyses were conducted upon vessels segmented from MRA images of the same patients using two tortuosity descriptors (SOAM and ICM), which have previously been demonstrated to have efficacy in separating benign from malignant disease. Linear regression analyses were conducted to determine if correlations exist between CBV or CBF and the two tortuosity measurements. For the overall set of tumors, no significant correlations were found between flow or volume measures and the tortuosity measures. However, when the 7 glioblastoma multiforme tumors were examined as a subgroup, the following significant correlations were found: rCBV and SOAM (R2=0.799), rCBV and ICM (R2=0.214). Our results demonstrate that MR perfusion imaging data do not correlate significantly with vessel tortuosity parameters as determined from the larger vessels seen by MRA. However, for subgroups of a particular tumor type such as GBM, there may be significant correlations. It appears that perfusion and tortuosity data may provide independently useful data in the assessment of cerebral neoplasms.

Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions.

BACKGROUND: Amoebae and bacteria interact within predator-prey and host-pathogen relationships, but the general response of amoeba to bacteria is not well understood. The amoeba Dictyostelium discoideum feeds on, and is colonized by, diverse bacterial species, including Gram-positive [Gram(+)] and Gram-negative [Gram(-)] bacteria, two major groups of bacteria that differ in structure and macromolecular composition. RESULTS: Transcriptional profiling of D. discoideum revealed sets of genes whose expression is enriched in amoebae interacting with different species of bacteria, including sets that appear specific to amoebae interacting with Gram(+) or with Gram(-) bacteria. In a genetic screen utilizing the growth of mutant amoebae on a variety of bacteria as a phenotypic readout, we identified amoebal genes that are only required for growth on Gram(+) bacteria, including one that encodes the cell-surface protein gp130, as well as several genes that are only required for growth on Gram(-) bacteria, including one that encodes a putative lysozyme, AlyL. These genes are required for parts of the transcriptional response of wild-type amoebae, and this allowed their classification into potential response pathways. CONCLUSIONS: We have defined genes that are critical for amoebal survival during feeding on Gram(+), or Gram(-), bacteria that we propose form part of a regulatory network that allows D. discoideum to elicit specific cellular responses to different species of bacteria in order to optimize survival.

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.

BACKGROUND: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. RESULTS: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. CONCLUSIONS: The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.

Conserved developmental transcriptomes in evolutionarily divergent species.

BACKGROUND: Evolutionarily divergent organisms often share developmental anatomies despite vast differences between their genome sequences. The social amoebae Dictyostelium discoideum and Dictyostelium purpureum have similar developmental morphologies although their genomes are as divergent as those of man and jawed fish. RESULTS: Here we show that the anatomical similarities are accompanied by extensive transcriptome conservation. Using RNA sequencing we compared the abundance and developmental regulation of all the transcripts in the two species. In both species, most genes are developmentally regulated and the greatest expression changes occur during the transition from unicellularity to multicellularity. The developmental regulation of transcription is highly conserved between orthologs in the two species. In addition to timing of expression, the level of mRNA production is also conserved between orthologs and is consistent with the intuitive notion that transcript abundance correlates with the amount of protein required. Furthermore, the conservation of transcriptomes extends to cell-type specific expression. CONCLUSIONS: These findings suggest that developmental programs are remarkably conserved at the transcriptome level, considering the great evolutionary distance between the genomes. Moreover, this transcriptional conservation may be responsible for the similar developmental anatomies of Dictyostelium discoideum and Dictyostelium purpureum.

Treatment of left main coronary trifurcation lesions with the paclitaxel drug-eluting stent: mid-term outcomes from a tertiary medical center.

BACKGROUND: Left main trifurcating coronary artery disease (LMTCAD) is a complex and challenging anatomy to treat percutaneously. We report on the immediate- and mid-term outcomes of 52 consecutive patients with LMTCAD treated with the Taxus(R) paclitaxel- eluting stent (PES) (Boston Scientific Corp., Natick, Mass.) in our center over a period of 2 years. METHODS: All patients (n = 52) who underwent LMTCAD at our center in 2006-2007 and treated with the PES form the basis of this report. Demographic, clinical, procedural and in-hospital outcome variables were reviewed. Angiograms were analyzed by an operator blinded to the patients' history. Mid-term follow up was achieved from medical records and/or phone calls. The primary endpoint of the study was either cardiac death, nonfatal myocardial infarction or target lesion revascularization (TLR) on follow up. Follow up was achieved in 47/51 patients (92.2%) at a mean of 292.8 +/- 104.6 days. Patients were classified as Type A (30.8%) disease involving the LM and origin of branches, or Type B (69.2%) disease involving the origin of the trifurcation branches only, but not the LM artery. All patients were treated with kissing balloon after stenting. Descriptive analysis was performed on all variables with mean +/- standard deviation for continuous variables and percentages describing dichotomous variables. Univariate and logistic regression analyses were performed to determine the predictors of the primary endpoint. RESULTS: The mean patient age was 67.6 +/- 12.7 years. The LM artery was unprotected in 88.5% of cases. On follow up, the primary endpoint was met in 34% of patients. TLR occurred in 31.9% of patients, and target vessel revascularization (TVR) in 40.4%. One patient had cardiac death (2.1%) 5 months after the index procedure, possibly related to acute stent thrombosis. By univariate analysis, Type A lesions (vs. Type B; p = 0.02) and the placement of a greater number of stents (p = 0.044) correlated with a higher event rate. Logistic regression analysis showed that Type A lesions are the only predictors of the combined endpoint (p = 0.011). CONCLUSION: LM trifurcation stenting carries an overall high rate of adverse events, mostly driven by a high TLR rate. Type A lesions and the number of stents placed predicted a higher combined endpoint of death, nonfatal MI and TLR. By logistic regression analysis, Type A lesions are the only independent predictors of the primary outcome.