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Background: Neoantigen-targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies have been initiated globally. Accurate identification and prioritization of neoantigens is crucial for designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example, limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression, and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address., Results: We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select, and export their neoantigen candidates. The tool allows users to visualize candidates at multiple levels of detail including variant, transcript, peptide, and algorithm prediction information., Conclusions: pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings. The application is available as part of the pVACtools software at pvactools.org and as an online server at pvacview.org., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests M.G. reports consulting fees from Jaime Leandro Foundation for Cancer Vaccines, Rare Cancer Research Foundation, and H37 and is on the Board of Directors of the Jaime Leandro Foundation for Cancer Vaccines. O.L.G. reports consulting fees from Jaime Leandro Foundation and is on the Board of Directors of the Cancer Genomics Consortium., (© 2024. The Author(s).)

Background: Neoantigen vaccines can induce or enhance highly specific antitumor immune responses with minimal risk of autoimmunity. We have developed a neoantigen DNA vaccine platform capable of efficiently presenting both HLA class I and II epitopes and performed a phase 1 clinical trial in triple-negative breast cancer patients with persistent disease on surgical pathology following neoadjuvant chemotherapy, a patient population at high risk of disease recurrence., Methods: Expressed somatic mutations were identified by tumor/normal exome sequencing and tumor RNA sequencing. The pVACtools software suite of neoantigen prediction algorithms was used to identify and prioritize cancer neoantigens and facilitate vaccine design for manufacture in an academic GMP facility. Neoantigen DNA vaccines were administered via electroporation in the adjuvant setting (i.e., following surgical removal of the primary tumor and completion of standard of care therapy). Vaccines were monitored for safety and immune responses via ELISpot, intracellular cytokine production via flow cytometry, and TCR sequencing., Results: Eighteen subjects received three doses of a neoantigen DNA vaccine encoding on average 11 neoantigens per patient (range 4-20). The vaccinations were well tolerated with relatively few adverse events. Neoantigen-specific T cell responses were induced in 14/18 patients as measured by ELISpot and flow cytometry. At a median follow-up of 36 months, recurrence-free survival was 87.5% (95% CI: 72.7-100%) in the cohort of vaccinated patients., Conclusion: Our study demonstrates neoantigen DNA vaccines are safe, feasible, and capable of inducing neoantigen-specific immune responses., Clinical Trial Registration Number: NCT02348320., Competing Interests: Declarations Ethics approval and consent to participate The clinical protocol was reviewed and approved by the Institutional Review Board (ID# 201505074) at Washington University School of Medicine. The research conformed to the principles of the Helsinki/Tokyo/Venice Declaration on experimentation in humans. Consent for publication Written consent for publication was obtained from all participating patients. Competing interests K.S., M.G., and O.G. are consultants for the Jaime Leandro Foundation. All other authors declare that they have no competing interests., (© 2024. The Author(s).)

Abstract: Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR repertoire from healthy individuals using RNA-seq data. An average of 52 somatic mutations per patient (range, 2-172) were identified, and ≥2 (median, 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all 4 patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field. This trial was registered at www.ClinicalTrials.gov as #NCT03121677., (© 2024 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Opinion Statement: Cardiac dysfunction is a serious adverse effect of cancer therapies that can interfere with quality of life and impact long-term survival in patients with cancer. Hematopoietic cell transplantation is a potentially curative therapy for many advanced hematologic malignancies and bone marrow failure syndromes, however is associated with several short- and long-term adverse effects, including importantly, cardiovascular toxicities. The goal of this review article is to describe the cardiovascular events that may develop before, during, and after hematopoietic cell transplantation, review risk factors for short- and long-term cardiovascular toxicities, discuss approaches to cardiovascular risk stratification and evaluation, and highlight the research gaps in the consideration of cardiovascular disease in patients undergoing hematopoietic cell transplantation. Further understanding of cardiovascular events and the factors associated with cardiovascular disease will hopefully lead to novel interventions in managing and mitigating the significant long-term burden of late cardiovascular effects in transplant survivors., (© 2024. The Author(s).)

In today's ever-changing world, adaptability is a key skill that is required to successfully navigate life's challenges. Through play individuals can build their innovation and adaptability skills. Additionally, through play we are able to collaborate with others and this builds connection amongst groups. And lastly, through practices such as gratitude we can increase our resilience skills when faced with life stressors.

Introduction: Glioblastoma multiforme is the most common and aggressive type of central nervous system tumor. We present a novel case of the challenges of dosing temozolomide in a patient with end stage renal disease on peritoneal hemodialysis with unpredictable clearance and toxicities., Case Report: In this case, a 60-year-old male with a past medical history of hypertension and Stage V chronic kidney disease presented with worsening confusion and word-finding difficulty in the emergency department. Magnetic resonance imaging demonstrated a large intra-axial mass within the posterior left frontal lobe measuring 4.5 × 4.1 × 3.5 cm with irregularly, predominant peripheral tumoral enhancement., Management and Outcome: The patient underwent a surgical resection which confirmed the diagnosis of glioblastoma (grade 4). The standard treatment for glioblastoma is 6 weeks of radiation therapy and daily temozolomide. Given his history of renal dysfunction and limited data on the safety of temozolomide in patients on hemodialysis (HD), the patient was administered dose-reduced temozolomide and closely monitored for toxicities. Temozolomide was successfully up-titrated to the full dose., Discussion: Renal replacement therapy is a life-saving treatment for end-stage kidney disease patients. A stepwise increase in the dosage of temozolomide did not increase the risk of toxicity with HD. There are no studies with patients on temozolomide and peritoneal dialysis. Our case transitioned to peritoneal dialysis from HD without significant toxicity from temozolomide. As a more substantial proportion of the population becomes dialysis-dependent in the coming years, we need further studies to understand the safety profiles of chemotherapeutic agents in this complex subset of patients.

Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies. Neoantigen identification and prioritization relies on correctly predicting whether the presenting peptide sequence can successfully induce an immune response. Because most somatic mutations are single-nucleotide variants, changes between wild-type and mutated peptides are typically subtle and require cautious interpretation. A potentially underappreciated variable in neoantigen prediction pipelines is the mutation position within the peptide relative to its anchor positions for the patient's specific MHC molecules. Whereas a subset of peptide positions are presented to the T cell receptor for recognition, others are responsible for anchoring to the MHC, making these positional considerations critical for predicting T cell responses. We computationally predicted anchor positions for different peptide lengths for 328 common HLA alleles and identified unique anchoring patterns among them. Analysis of 923 tumor samples shows that 6 to 38% of neoantigen candidates are potentially misclassified and can be rescued using allele-specific knowledge of anchor positions. A subset of anchor results were orthogonally validated using protein crystallography structures. Representative anchor trends were experimentally validated using peptide-MHC stability assays and competition binding assays. By incorporating our anchor prediction results into neoantigen prediction pipelines, we hope to formalize, streamline, and improve the identification process for relevant clinical studies.

Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells 1-14 . The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies 15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8 + T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Purpose: Virtual medicine (VM) use increased during the COVID-19 pandemic as it represented a safe alternative to traditional face-to-face health care delivery. This prospective cross-sectional study aimed to characterize preferences and perceived barriers to VM on the basis of language and specific sociodemographic variables while also identifying particular subpopulations at risk of dissatisfaction regarding VM., Methods: An institutional review board-approved, 23-item questionnaire was offered in English and Spanish. Examined variables included demographic information, preferences, and perceived barriers regarding VM. Multivariable analysis was performed to determine the association between demographic variables and participants' preferences and perceived barriers., Results: Fewer Hispanic and underserved patients (N = 241) had received oncological care through VM (28.9% v 30.8%) despite comparable preferences and levels of satisfaction regarding the incorporation of VM in health care delivery (21.6% v 25.4%; 68.7% v 82.1%), respectively, with no significant difference by age, level of education, marital status, or Hispanic ethnicity, although Spanish as primary language was statistically significant ( P = .001). Although Hispanic and underserved rely more on social media to receive health information (26.5% v 24.7%), they have more technical barriers. They were up to 2.9 times more likely not to have a phone/iPad/similar or access broadband connectivity., Conclusion: Given the shift toward outpatient and home-based care, an aging population, and cultural appropriations, VM excitedly allows the reincorporation of family/caregiver in medical engagement. Hispanic patients are equally interested and satisfied in receiving oncological care through VM, but fewer are currently using it. Barriers are predominantly technical and targetable with appropriate policies to help overcome technological barriers on the basis of language, ethnic, locoregional, and sociodemographic variables.

Background: BrightArm Compact is a new rehabilitation system for the upper extremities. It provides bimanual training with gradated gravity loading and mediates interactions with cognitively challenging serious games., Objective: The aim of this study is to design and test a robotic rehabilitation table-based virtual rehabilitation system for functional impact of the integrative training in the early poststroke phase., Methods: A new robotic rehabilitation table, controllers, and adaptive games were developed. The 2 participants underwent 12 experimental sessions in addition to the standard of care. Standardized measures of upper extremity function (primary outcome), depression, and cognition were administered before and after the intervention. Nonstandardized measures included game variables and subjective evaluations., Results: The 2 case study participants attained high total arm repetitions per session (504 and 957) and achieved high grasp and finger-extension counts. Training intensity contributed to marked improvements in affected shoulder strength (225% and 100% increase), grasp strength (27% and 16% increase), and pinch strength (31% and 15% increase). The shoulder flexion range increased by 17% and 18% and elbow supination range by 75% and 58%. Improvements in motor function were at or above minimal clinically important difference for the Fugl-Meyer Assessment (11 and 10 points), Chedoke Arm and Hand Activity Inventory (11 and 14 points), and Upper Extremity Functional Index (19 and 23 points). Cognitive and emotive outcomes were mixed. Subjective rating by participants and training therapists were positive (average 4, SD 0.22, on a 5-point Likert scale)., Conclusions: The design of the robotic rehabilitation table was tested on 2 participants in the early poststroke phase, and results are encouraging for upper extremity functional gains and technology acceptance., Trial Registration: ClinicalTrials.gov NCT04252170; https://clinicaltrials.gov/ct2/show/NCT04252170., (©Grigore Burdea, Nam Kim, Kevin Polistico, Ashwin Kadaru, Namrata Grampurohit, Jasdeep Hundal, Simcha Pollack. Originally published in JMIR Rehabilitation and Assistive Technology (https://rehab.jmir.org), 13.04.2022.)

Growing interest in quantum computing for practical applications has led to a surge in the availability of programmable machines for executing quantum algorithms 1,2 . Present-day photonic quantum computers 3-7 have been limited either to non-deterministic operation, low photon numbers and rates, or fixed random gate sequences. Here we introduce a full-stack hardware-software system for executing many-photon quantum circuit operations using integrated nanophotonics: a programmable chip, operating at room temperature and interfaced with a fully automated control system. The system enables remote users to execute quantum algorithms that require up to eight modes of strongly squeezed vacuum initialized as two-mode squeezed states in single temporal modes, a fully general and programmable four-mode interferometer, and photon number-resolving readout on all outputs. Detection of multi-photon events with photon numbers and rates exceeding any previous programmable quantum optical demonstration is made possible by strong squeezing and high sampling rates. We verify the non-classicality of the device output, and use the platform to carry out proof-of-principle demonstrations of three quantum algorithms: Gaussian boson sampling, molecular vibronic spectra and graph similarity 8 . These demonstrations validate the platform as a launchpad for scaling photonic technologies for quantum information processing.

Amyloid of the ureter is a rare disease with less than 25 cases reported in the literature. Despite being rare, it remains an important entity as it is typically confused with a primary neoplastic process of the urinary system. We report a case of a 68-year-old male with a history of cutaneous amyloid with late presentation of bilateral ureteral involvement., (Copyright © 2020. Published by Elsevier Inc.)

In the midst of the COVID-19 pandemic, further understanding of its complications points towards dysregulated immune response as a major component. Systemic lupus erythematosus (SLE) is also a disease of immune dysregulation leading to multisystem compromise. We present a case of new-onset SLE concomitantly with COVID-19 and development of antiphospholipid antibodies. An 18-year-old female that presented with hemodynamic collapse and respiratory failure, progressed to cardiac arrest, and had a pericardial tamponade drained. She then progressed to severe acute respiratory distress syndrome, severe ventricular dysfunction, and worsening renal function with proteinuria and hematuria. Further studies showed bilateral pleural effusions, positive antinuclear and antidouble-stranded DNA antibodies, lupus anticoagulant, and anticardiolipin B. C3 and C4 levels were low. SARS-Cov-2 PCR was positive after 2 negative tests. She also developed multiple deep venous thrombosis, in the setting of positive antiphospholipid antibodies and lupus anticoagulant. In terms of pathophysiology, COVID-19 is believed to cause a dysregulated cytokine response which could potentially be exacerbated by the shift in Th1 to Th2 response seen in SLE. Also, it is well documented that viral infections are an environmental factor that contributes to the development of autoimmunity; however, COVID-19 is a new entity, and it is not known if it could trigger autoimmune conditions. Additionally, it is possible that SARS-CoV-2, as it happens with other viruses, might lead to the formation of antiphospholipid antibodies, potentially contributing to the increased rates of thrombosis seen in COVID-19.

Background: The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies., Methods: In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence., Results: A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies., Conclusions: Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens., Competing Interests: Disclosures J.B. is CEO and co-founder and J.C. is CSO and co-founder of AlbaJuna Therapeutics SL. N.M. has received consultancy fees from Achilles Therapeutics. L.D.M.A. has received honoraria for participation in a speaker's bureau/consultancy from Roche. V.G. is CTO and founder of Nostrum Biodiscovery. T.A.C is a co-founder of Gritstone Oncology and holds stock. T.A.C. has received grant support from BMS, AstraZeneca, Eisai, Illumina, An2H, and Pfizer. T.A.C has been on the scientific advisory boards of BMS, AstraZeneca, Merck, Illumina, and An2H. All remaining authors have declared no conflicts of interest., (Copyright © 2020 European Society for Medical Oncology. Published by Elsevier Ltd. All rights reserved.)

Identification of neoantigens is a critical step in predicting response to checkpoint blockade therapy and design of personalized cancer vaccines. This is a cross-disciplinary challenge, involving genomics, proteomics, immunology, and computational approaches. We have built a computational framework called pVACtools that, when paired with a well-established genomics pipeline, produces an end-to-end solution for neoantigen characterization. pVACtools supports identification of altered peptides from different mechanisms, including point mutations, in-frame and frameshift insertions and deletions, and gene fusions. Prediction of peptide:MHC binding is accomplished by supporting an ensemble of MHC Class I and II binding algorithms within a framework designed to facilitate the incorporation of additional algorithms. Prioritization of predicted peptides occurs by integrating diverse data, including mutant allele expression, peptide binding affinities, and determination whether a mutation is clonal or subclonal. Interactive visualization via a Web interface allows clinical users to efficiently generate, review, and interpret results, selecting candidate peptides for individual patient vaccine designs. Additional modules support design choices needed for competing vaccine delivery approaches. One such module optimizes peptide ordering to minimize junctional epitopes in DNA vector vaccines. Downstream analysis commands for synthetic long peptide vaccines are available to assess candidates for factors that influence peptide synthesis. All of the aforementioned steps are executed via a modular workflow consisting of tools for neoantigen prediction from somatic alterations (pVACseq and pVACfuse), prioritization, and selection using a graphical Web-based interface (pVACviz), and design of DNA vector-based vaccines (pVACvector) and synthetic long peptide vaccines. pVACtools is available at http://www.pvactools.org., (©2020 American Association for Cancer Research.)

The impact of intratumoral heterogeneity (ITH) and the resultant neoantigen landscape on T cell immunity are poorly understood. ITH is a widely recognized feature of solid tumors and poses distinct challenges related to the development of effective therapeutic strategies, including cancer neoantigen vaccines. Here, we performed deep targeted DNA sequencing of multiple metastases from melanoma patients and observed ubiquitous sharing of clonal and subclonal single nucleotide variants (SNVs) encoding putative HLA class I-restricted neoantigen epitopes. However, spontaneous antitumor CD8+ T cell immunity in peripheral blood and tumors was restricted to a few clonal neoantigens featuring an oligo-/monoclonal T cell-receptor (TCR) repertoire. Moreover, in various tumors of the 4 patients examined, no neoantigen-specific TCR clonotypes were identified despite clonal neoantigen expression. Mature dendritic cell (mDC) vaccination with tumor-encoded amino acid-substituted (AAS) peptides revealed diverse neoantigen-specific CD8+ T responses, each composed of multiple TCR clonotypes. Isolation of T cell clones by limiting dilution from tumor-infiltrating lymphocytes (TILs) permitted functional validation regarding neoantigen specificity. Gene transfer of TCRαβ heterodimers specific for clonal neoantigens confirmed correct TCR clonotype assignments based on high-throughput TCRBV CDR3 sequencing. Our findings implicate immunological ignorance of clonal neoantigens as the basis for ineffective T cell immunity to melanoma and support the concept that therapeutic vaccination, as an adjunct to checkpoint inhibitor treatment, is required to increase the breadth and diversity of neoantigen-specific CD8+ T cells., Competing Interests: The authors declare no competing interest.

Purpose: Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability., Methods: This manual review standard operating procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer's confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing., Results: After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time., Conclusion: This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.

Recent efforts to design personalized cancer immunotherapies use predicted neoantigens, but most neoantigen prediction strategies do not consider proximal (nearby) variants that alter the peptide sequence and may influence neoantigen binding. We evaluated somatic variants from 430 tumors to understand how proximal somatic and germline alterations change the neoantigenic peptide sequence and also affect neoantigen binding predictions. On average, 241 missense somatic variants were analyzed per sample. Of these somatic variants, 5% had one or more in-phase missense proximal variants. Without incorporating proximal variant correction for major histocompatibility complex class I neoantigen peptides, the overall false discovery rate (incorrect neoantigens predicted) and the false negative rate (strong-binding neoantigens missed) across peptides of lengths 8-11 were estimated as 0.069 (6.9%) and 0.026 (2.6%), respectively.

The original version of this Article contained errors in the depiction of confidence intervals in the NF1 BCSS data illustrated in Figure 3b. These have now been corrected in both the PDF and HTML versions of the Article. The incorrect version of Figure 3b is presented in the associated Author Correction.

Here we report targeted sequencing of 83 genes using DNA from primary breast cancer samples from 625 postmenopausal (UBC-TAM series) and 328 premenopausal (MA12 trial) hormone receptor-positive (HR+) patients to determine interactions between somatic mutation and prognosis. Independent validation of prognostic interactions was achieved using data from the METABRIC study. Previously established associations between MAP3K1 and PIK3CA mutations with luminal A status/favorable prognosis and TP53 mutations with Luminal B/non-luminal tumors/poor prognosis were observed, validating the methodological approach. In UBC-TAM, NF1 frame-shift nonsense (FS/NS) mutations were also a poor outcome driver that was validated in METABRIC. For MA12, poor outcome associated with PIK3R1 mutation was also reproducible. DDR1 mutations were strongly associated with poor prognosis in UBC-TAM despite stringent false discovery correction (q = 0.0003). In conclusion, uncommon recurrent somatic mutations should be further explored to create a more complete explanation of the highly variable outcomes that typifies ER+ breast cancer.

Importance: Limited evidence supports a link between hidradenitis suppurativa (HS) and Crohn disease (CD), and this relationship has not been established in the United States., Objective: To evaluate the prevalence of CD among patients with HS in the United States and to determine the strength of association between the 2 conditions., Design, Setting, and Participants: Cross-sectional analysis of data from 51 340 patients with HS identified using electronic health records data in the Explorys multiple health system data analytics and research platform, which includes data from more than 50 million unique patients across all US census regions., Main Outcomes and Measures: Primary outcome was diagnosis of CD., Results: Of the 18 455 660 total population considered, 51 340 had HS (35 000 women). Of these patients with HS, 29 010 (56.5%) were aged 18 to 44 years; 17 580 (34,2%), 45 to 64 years; and 4750 (9.3%), 65 years or older. Prevalence of CD among patients with HS was 2.0% (1025/51 340), compared with 0.6% (113 360/18 404 260) among those without HS (P < .001). Prevalence of CD was greatest among patients with HS who were white (2.3%), aged 45 to 64 years (2.4%), nonobese (2.8%), and tobacco smokers (2.3%). In univariable and multivariable analyses, patients with HS had 3.29 (95% CI, 3.09-3.50) and 3.05 (95% CI, 2.87-3.25) times the odds of having CD, respectively, compared with patients without HS. Crohn disease was associated with HS across all patient subgroups. The association was strongest for men (OR, 3.61; 95% CI, 3.24-4.03), patients aged 45 to 64 years (OR, 3.49; 95% CI, 3.16-3.85), nonobese patients (OR, 4.09; 95% CI, 3.69-4.54), and nonsmokers (OR, 3.44; 95% CI, 3.10-3.82)., Conclusions and Relevance: These data suggest that patients with HS are at risk for CD. Gastrointestinal symptoms or signs suggestive of CD warrant additional evaluation by a gastroenterologist.

Next-generation sequencing technologies have provided insights into the biology and mutational landscape of cancer. Here, we evaluate the relevance of cancer neoantigens in human breast cancers. Using patient-derived xenografts from three patients with advanced breast cancer (xenografts were designated as WHIM30, WHIM35, and WHIM37), we sequenced exomes of tumor and patient-matched normal cells. We identified 2,091 (WHIM30), 354 (WHIM35), and 235 (WHIM37) nonsynonymous somatic mutations. A computational analysis identified and prioritized HLA class I-restricted candidate neoantigens expressed in the dominant tumor clone. Each candidate neoantigen was evaluated using peptide-binding assays, T-cell cultures that measure the ability of CD8 + T cells to recognize candidate neoantigens, and preclinical models in which we measured antitumor immunity. Our results demonstrate that breast cancer neoantigens can be recognized by the immune system, and that human CD8 + T cells enriched for prioritized breast cancer neoantigens were able to protect mice from tumor challenge with autologous patient-derived xenografts. We conclude that next-generation sequencing and epitope-prediction strategies can identify and prioritize candidate neoantigens for immune targeting in breast cancer. Cancer Immunol Res; 5(7); 516-23. ©2017 AACR ., (©2017 American Association for Cancer Research.)

Background: HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference., Patients and Methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483). We have extracted genomic DNA from both pre-treatment tumor biopsies and blood of these 48 cases, and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have generated RNA-seq profiles from 42 of the tumor biopsies. Among patients in this cohort, 24 (50%) achieved a pCR., Results: We have characterized the genomic landscape of HER2-positive breast cancer and investigated associations between genomic features and pCR. Cases assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR compared to the luminal, basal-like, or normal-like subtypes (19/27 versus 3/15; P = 0.0032). Mutational events led to the generation of putatively active neoantigens, but were overall not associated with pCR. ERBB2 and GRB7 were the genes most commonly observed in fusion events, and genomic copy number analysis of the ERBB2 locus indicated that cases with either no observable or low-level ERBB2 amplification were less likely to achieve a pCR (7/8 versus 17/40; P = 0.048). Moreover, among cases that achieved a pCR, tumors consistently expressed immune signatures that may contribute to therapeutic response., Conclusion: The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those HER2-positive breast cancer patients who will not respond to treatment with chemotherapy and trastuzumab., Clinicaltrials.gov Identifiers: NCT00513292, NCT00353483., (© The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Antibody blockade of programmed death-1 (PD-1) or its ligand, PD-L1, has led to unprecedented therapeutic responses in certain tumor-bearing individuals, but PD-L1 expression's prognostic value in stratifying cancer patients for such treatment remains unclear. Reports conflict on the significance of correlations between PD-L1 on tumor cells and positive clinical outcomes to PD-1/PD-L1 blockade. We investigated this issue using genomically related, clonal subsets from the same methylcholanthrene-induced sarcoma: a highly immunogenic subset that is spontaneously eliminated in vivo by adaptive immunity and a less immunogenic subset that forms tumors in immunocompetent mice, but is sensitive to PD-1/PD-L1 blockade therapy. Using CRISPR/Cas9-induced loss-of-function approaches and overexpression gain-of-function techniques, we confirmed that PD-L1 on tumor cells is key to promoting tumor escape. In addition, the capacity of PD-L1 to suppress antitumor responses was inversely proportional to tumor cell antigenicity. PD-L1 expression on host cells, particularly tumor-associated macrophages (TAM), was also important for tumor immune escape. We demonstrated that induction of PD-L1 on tumor cells was IFNγ-dependent and transient, but PD-L1 induction on TAMs was of greater magnitude, only partially IFNγ dependent, and was stable over time. Thus, PD-L1 expression on either tumor cells or host immune cells could lead to tumor escape from immune control, indicating that total PD-L1 expression in the immediate tumor microenvironment may represent a more accurate biomarker for predicting response to PD-1/PD-L1 blockade therapy, compared with monitoring PD-L1 expression on tumor cells alone. Cancer Immunol Res; 5(2); 106-17. ©2017 AACR., (©2017 American Association for Cancer Research.)

Background: Persistent pain in shoulder and arm following post-surgical breast cancer treatment can lead to cognitive and physical deficits. Depression is also common in breast cancer survivors. Virtual reality therapy with integrative cognitive and physical rehabilitation has not been clinically trialed for this population. The novel BrightArm Duo technology improved cognition and upper extremity (UE) function for other diagnoses and has great potential to benefit individuals coping with post-surgical breast cancer pain., Objectives: The aim of this study was to explore the feasibility of BrightArm Duo therapy for coping with post-surgical chronic pain and associated disability in breast cancer survivors with depression., Methods: BrightArm Duo is a robotic rehabilitation table modulating gravity loading on supported forearms. It tracks arm position and grasping strength while patients play three-dimensional (3D) custom integrative rehabilitation games. Community-dwelling women (N = 6) with post-surgical breast cancer pain in the upper arm trained on the system twice a week for 8 weeks. Training difficulty increased progressively in game complexity, table tilt and session length (20-50 minutes). Standardized assessments were performed before and after therapy for pain, cognition, emotion, UE function and activities of daily living., Results: Subjects averaged upwards of 1300 arm repetitions and 850 hand grasps per session. Pain intensity showed a 20% downward trend (p = 0.1) that was corroborated by therapist observations and participant feedback. A total of 10 out of 11 cognitive metrics improved post-training (p = 0.01) with a significant 8.3-point reduction in depression severity (p = 0.04). A total of 17 of 18 range of motion metrics increased (p < 0.01), with five affected-side shoulder improvements above the Minimal Clinically Important Difference (8°). In all, 13 out of 15 strength and function metrics improved (p = 0.02) with lateral deltoid strength increasing 7.4 N on the affected side (p = 0.05)., Conclusion: This pilot study demonstrated feasibility of using the BrightArm Duo Rehabilitation System to treat cancer survivors coping with upper body chronic pain. Outcomes indicate improvement in cognition, shoulder range, strength, function and depression., Competing Interests: The authors declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: G.H. is CTO of Bright Cloud International Corp (BCI). G.B. is inventor on a patent related to technology described above and majority shareholder of BCI. N.G. is a part-time employee and K.P. is a full-time employee of BCI. D.R. is a part-time employee and shareholder of BCI. F.D. is an Administrator of Roosevelt Care Center where the project study took place. J.H. has been a contractor for BCI. D.D. is the founder of the University Pain Medicine Center that recruited the subjects for this study.

Purpose: To describe the novel BrightArm Duo bimanual upper extremity (UE) rehabilitation system; to determine its technology acceptance and clinical benefit for older hemiplegic participants., Methods: The system table tilted to adjust arm gravity loading. Participants wore arm supports that sensed grasp strength and wrist position on the table. Wrist weights further increased shoulder exertion. Games were designed to improve UE strength, motor function, cognition and emotive state and adapted automatically to each participant. The system underwent feasibility trials spanning 8 weeks in two skilled nursing facilities (SNFs). Participants were evaluated pre-therapy and post-therapy using standardized clinical measures. Computerized measures of supported arm reach, table tilt and number of arm repetitions were stored on a remote server., Outcomes: Seven participants had significant improvements in their active range of shoulder movement, supported arm reach, shoulder strength, grasp strength and their ability to focus. The group demonstrated higher arm function measured with FMA (p = 0.01) and CAHAI (p = 0.05), and had an improvement in depression (Becks Depression Inventory, II). BrightArm Duo technology was well accepted by participants with a rating of 4.4 out of 5 points., Conclusions: Given these findings, it will be beneficial to evaluate the BrightArm Duo application in SNF maintenance programs. Implications for Rehabilitation Integrative rehabilitation that addresses both physical and cognitive domains is promising for post-stroke maintenance in skilled nursing facilities. Simultaneous bilateral arm exercise may improve arm function in older hemiplegic patients several years after stroke. Virtual reality games that adapt to the patient can increase attention and working memory while decreasing depression in elderly.

Estrogen receptor alpha-positive (ERα+) luminal tumors are the most frequent subtype of breast cancer. Stat1(-/-) mice develop mammary tumors that closely recapitulate the biological characteristics of this cancer subtype. To identify transforming events that contribute to tumorigenesis, we performed whole genome sequencing of Stat1(-/-) primary mammary tumors and matched normal tissues. This investigation identified somatic truncating mutations affecting the prolactin receptor (PRLR) in all tumor and no normal samples. Targeted sequencing confirmed the presence of these mutations in precancerous lesions, indicating that this is an early event in tumorigenesis. Functional evaluation of these heterozygous mutations in Stat1(-/-) mouse embryonic fibroblasts showed that co-expression of truncated and wild-type PRLR led to aberrant STAT3 and STAT5 activation downstream of the receptor, cellular transformation in vitro, and tumor formation in vivo. In conclusion, truncating mutations of PRLR promote tumor growth in a model of human ERα+ breast cancer and warrant further investigation., (Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.)

The genomic events responsible for the pathogenesis of relapsed adult B-lymphoblastic leukemia (B-ALL) are not yet clear. We performed integrative analysis of whole-genome, whole-exome, custom capture, whole-transcriptome (RNA-seq), and locus-specific genomic assays across nine time points from a patient with primary de novo B-ALL. Comprehensive genome and transcriptome characterization revealed a dramatic tumor evolution during progression, yielding a tumor with complex clonal architecture at second relapse. We observed and validated point mutations in EP300 and NF1, a highly expressed EP300-ZNF384 gene fusion, a microdeletion in IKZF1, a focal deletion affecting SETD2, and large deletions affecting RB1, PAX5, NF1, and ETV6. Although the genome analysis revealed events of potential biological relevance, no clinically actionable treatment options were evident at the time of the second relapse. However, transcriptome analysis identified aberrant overexpression of the targetable protein kinase encoded by the FLT3 gene. Although the patient had refractory disease after salvage therapy for the second relapse, treatment with the FLT3 inhibitor sunitinib rapidly induced a near complete molecular response, permitting the patient to proceed to a matched-unrelated donor stem cell transplantation. The patient remains in complete remission more than 4 years later. Analysis of this patient's relapse genome revealed an unexpected, actionable therapeutic target that led to a specific therapy associated with a rapid clinical response. For some patients with relapsed or refractory cancers, this approach may indicate a novel therapeutic intervention that could alter outcome., (Copyright © 2016 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.)

Purpose: This study describes the BrightArm™ Duo virtual reality system (Bright Cloud International Corp., Highland Park, NJ) and determines its clinical benefit for maintenance of upper extremity function in nursing home residents who are chronic poststroke., Materials and Methods: Participants sat at a low-friction robotic table with tilt and lift capability and interacted with serious games through computerized supports that measured forearm movement and grasp. The rehabilitation simulations were designed to improve arm and hand function, increase range of motion, and improve emotional well-being and cognition (attention, memory, and executive functioning). After 8 weeks of initial intensive therapy, there were three booster periods at 8-week intervals, each consisting of four sessions over 2 weeks. The last booster was a tournament competition, where pairs of residents played games collaboratively from remote nursing homes. Participants were evaluated before and after each booster period using standardized clinical measures., Results: Range of motion improved for 18 out of 23 upper extremity movement variables (P = 0.01) between pre- and post-tournament assessment, and the residents self-reported that they enjoyed playing with a partner (score of 4.7 out of 5.0). Participants were able to reduce game completion time through cooperative play (teamwork), and the times improved with successive sessions of the tournament. Affected hand and arm function and depression levels were maintained (no decline) after the tournament., Conclusions: A rehabilitation tournament using virtual reality between teams of nursing home residents chronic poststroke is the first of its kind in clinical practice. This study demonstrates its effectiveness in improving range of motion of the upper extremity while engaging residents in the maintenance program at their nursing home.

Cancer immunotherapy has gained significant momentum from recent clinical successes of checkpoint blockade inhibition. Massively parallel sequence analysis suggests a connection between mutational load and response to this class of therapy. Methods to identify which tumor-specific mutant peptides (neoantigens) can elicit anti-tumor T cell immunity are needed to improve predictions of checkpoint therapy response and to identify targets for vaccines and adoptive T cell therapies. Here, we present a flexible, streamlined computational workflow for identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). pVAC-Seq is available at https://github.com/griffithlab/pVAC-Seq .

The application of modern high-throughput genomics to the study of cancer genomes has exploded in the past few years, yielding unanticipated insights into the myriad and complex combinations of genomic alterations that lead to the development of cancers. Coincident with these genomic approaches have been computational analyses that are capable of multiplex evaluations of genomic data toward specific therapeutic end points. One such approach is called "immunogenomics" and is now being developed to interpret protein-altering changes in cancer cells in the context of predicted preferential binding of these altered peptides by the patient's immune molecules, specifically human leukocyte antigen (HLA) class I and II proteins. One goal of immunogenomics is to identify those cancer-specific alterations that are likely to elicit an immune response that is highly specific to the patient's cancer cells following stimulation by a personalized vaccine. The elements of such an approach are outlined herein and constitute an emerging therapeutic option for cancer patients., (© 2016 Hundal et al; Published by Cold Spring Harbor Laboratory Press.)

Importance: Tests that predict outcomes for patients with acute myeloid leukemia (AML) are imprecise, especially for those with intermediate risk AML., Objectives: To determine whether genomic approaches can provide novel prognostic information for adult patients with de novo AML., Design, Setting, and Participants: Whole-genome or exome sequencing was performed on samples obtained at disease presentation from 71 patients with AML (mean age, 50.8 years) treated with standard induction chemotherapy at a single site starting in March 2002, with follow-up through January 2015. In addition, deep digital sequencing was performed on paired diagnosis and remission samples from 50 patients (including 32 with intermediate-risk AML), approximately 30 days after successful induction therapy. Twenty-five of the 50 were from the cohort of 71 patients, and 25 were new, additional cases., Exposures: Whole-genome or exome sequencing and targeted deep sequencing. Risk of identification based on genetic data., Main Outcomes and Measures: Mutation patterns (including clearance of leukemia-associated variants after chemotherapy) and their association with event-free survival and overall survival., Results: Analysis of comprehensive genomic data from the 71 patients did not improve outcome assessment over current standard-of-care metrics. In an analysis of 50 patients with both presentation and documented remission samples, 24 (48%) had persistent leukemia-associated mutations in at least 5% of bone marrow cells at remission. The 24 with persistent mutations had significantly reduced event-free and overall survival vs the 26 who cleared all mutations. Patients with intermediate cytogenetic risk profiles had similar findings. [table: see text]., Conclusions and Relevance: The detection of persistent leukemia-associated mutations in at least 5% of bone marrow cells in day 30 remission samples was associated with a significantly increased risk of relapse, and reduced overall survival. These data suggest that this genomic approach may improve risk stratification for patients with AML.

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

T cell immunity directed against tumor-encoded amino acid substitutions occurs in some melanoma patients. This implicates missense mutations as a source of patient-specific neoantigens. However, a systematic evaluation of these putative neoantigens as targets of antitumor immunity is lacking. Moreover, it remains unknown whether vaccination can augment such responses. We found that a dendritic cell vaccine led to an increase in naturally occurring neoantigen-specific immunity and revealed previously undetected human leukocyte antigen (HLA) class I-restricted neoantigens in patients with advanced melanoma. The presentation of neoantigens by HLA-A*02:01 in human melanoma was confirmed by mass spectrometry. Vaccination promoted a diverse neoantigen-specific T cell receptor (TCR) repertoire in terms of both TCR-β usage and clonal composition. Our results demonstrate that vaccination directed at tumor-encoded amino acid substitutions broadens the antigenic breadth and clonal diversity of antitumor immunity., (Copyright © 2015, American Association for the Advancement of Science.)

We previously identified missense mutations in the U2AF1 splicing factor affecting codons S34 (S34F and S34Y) or Q157 (Q157R and Q157P) in 11% of the patients with de novo myelodysplastic syndrome (MDS). Although the role of U2AF1 as an accessory factor in the U2 snRNP is well established, it is not yet clear how these mutations affect splicing or contribute to MDS pathophysiology. We analyzed splice junctions in RNA-seq data generated from transfected CD34+ hematopoietic cells and found significant differences in the abundance of known and novel junctions in samples expressing mutant U2AF1 (S34F). For selected transcripts, splicing alterations detected by RNA-seq were confirmed by analysis of primary de novo MDS patient samples. These effects were not due to impaired U2AF1 (S34F) localization as it co-localized normally with U2AF2 within nuclear speckles. We further found evidence in the RNA-seq data for decreased affinity of U2AF1 (S34F) for uridine (relative to cytidine) at the e-3 position immediately upstream of the splice acceptor site and corroborated this finding using affinity-binding assays. These data suggest that the S34F mutation alters U2AF1 function in the context of specific RNA sequences, leading to aberrant alternative splicing of target genes, some of which may be relevant for MDS pathogenesis.

Therapy-related acute myeloid leukaemia (t-AML) and therapy-related myelodysplastic syndrome (t-MDS) are well-recognized complications of cytotoxic chemotherapy and/or radiotherapy. There are several features that distinguish t-AML from de novo AML, including a higher incidence of TP53 mutations, abnormalities of chromosomes 5 or 7, complex cytogenetics and a reduced response to chemotherapy. However, it is not clear how prior exposure to cytotoxic therapy influences leukaemogenesis. In particular, the mechanism by which TP53 mutations are selectively enriched in t-AML/t-MDS is unknown. Here, by sequencing the genomes of 22 patients with t-AML, we show that the total number of somatic single-nucleotide variants and the percentage of chemotherapy-related transversions are similar in t-AML and de novo AML, indicating that previous chemotherapy does not induce genome-wide DNA damage. We identified four cases of t-AML/t-MDS in which the exact TP53 mutation found at diagnosis was also present at low frequencies (0.003-0.7%) in mobilized blood leukocytes or bone marrow 3-6 years before the development of t-AML/t-MDS, including two cases in which the relevant TP53 mutation was detected before any chemotherapy. Moreover, functional TP53 mutations were identified in small populations of peripheral blood cells of healthy chemotherapy-naive elderly individuals. Finally, in mouse bone marrow chimaeras containing both wild-type and Tp53(+/-) haematopoietic stem/progenitor cells (HSPCs), the Tp53(+/-) HSPCs preferentially expanded after exposure to chemotherapy. These data suggest that cytotoxic therapy does not directly induce TP53 mutations. Rather, they support a model in which rare HSPCs carrying age-related TP53 mutations are resistant to chemotherapy and expand preferentially after treatment. The early acquisition of TP53 mutations in the founding HSPC clone probably contributes to the frequent cytogenetic abnormalities and poor responses to chemotherapy that are typical of patients with t-AML/t-MDS.

Genome sequencing studies of patient samples have implicated the involvement of various components of the epigenetic machinery in myeloid diseases, including the de novo DNA methyltransferase DNMT3A. We have recently shown that Dnmt3a is essential for hematopoietic stem cell differentiation. Here, we investigated the effect of loss of Dnmt3a on hematopoietic transformation by forcing the normally quiescent hematopoietic stem cells to divide in vivo. Mice transplanted with Dnmt3a-null bone marrow in the absence of wildtype support cells succumbed to bone marrow failure (median survival, 328 days) characteristic of myelodysplastic syndromes with symptoms including anemia, neutropenia, bone marrow hypercellularity, and splenomegaly with myeloid infiltration. Two out of 25 mice developed myeloid leukemia with >20%blasts in the blood and bone marrow. Four out of 25 primary mice succumbed to myeloproliferative disorders, some of which progressed to secondary leukemia after long latency. Exome sequencing identified cooperating c-Kit mutations found only in the leukemic samples. Ectopic introduction of c-Kit variants into a Dnmt3a-deficient background produced acute leukemia with a short latency (median survival, 67 days). Our data highlight crucial roles of Dnmt3a in normal and malignant hematopoiesis and suggest that a major role for this enzyme is to facilitate developmental progression of progenitor cells at multiple decision checkpoints.