Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.

Cellular senescence suppresses cancer by irreversibly arresting cell proliferation. Senescent cells acquire a pro-inflammatory senescence-associated secretory phenotype. Many genotoxic chemotherapies target proliferating cells non-specifically, often with adverse reactions. In accord with prior work, we show that several chemotherapeutic drugs induce senescence of primary murine and human cells. Using a transgenic mouse that permits tracking and eliminating senescent cells, we show that therapy-induced senescent (TIS) cells persist and contribute to local and systemic inflammation. Eliminating TIS cells reduced several short- and long-term effects of the drugs, including bone marrow suppression, cardiac dysfunction, cancer recurrence and physical activity and strength. Consistent with our findings in mice, the risk of chemotherapy-induced fatigue was significantly greater in humans with increased expression of a senescence marker in T-cells prior to chemotherapy. These findings suggest that senescent cells can cause certain chemotherapy side effects, providing a new target to reduce the toxicity of anti-cancer treatments.

The recent successes of immunotherapy have shifted the paradigm in cancer treatment but since only a percentage of patients respond, it is imperative to identify factors impacting outcome. Obesity is reaching pandemic proportions and is a major risk factor for certain malignancies, but the impact of obesity on immune responses, in general, and in cancer immunotherapy, in particular, is poorly understood. Here we demonstrate, across multiple species and tumor models, that obesity results in increased immune aging, tumor progression and PD-1-mediated T cell dysfunction which is driven, at least in part, by leptin. Strikingly however, obesity is also associated with increased efficacy of PD-1/PD-L1 blockade in both tumor-bearing mice and clinical cancer patients. These findings advance our understanding of obesity-induced immune dysfunction and its consequences in cancer and highlight obesity as a biomarker for some cancer immunotherapies. These data indicate a paradoxical impact of obesity on cancer. There is heightened immune dysfunction and tumor progression but also greater anti-tumor efficacy and survival following checkpoint blockade which directly targets some of the pathways activated in obesity.

The efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is limited by acute and chronic graft-versus-host disease (GVHD). The impact of obesity on allo-HSCT outcomes is poorly understood. Here, we report that obesity had a negative and selective impact on acute gut GVHD after allo-HSCT in mice with diet-induced obesity (DIO). These animals exhibited increased gut permeability, endotoxin translocation across the gut, and radiation-induced gastrointestinal damage after allo-HSCT. After allo-HSCT, both male and female DIO mouse recipients showed increased proinflammatory cytokine production and expression of the GVHD marker ST2 (IL-33R) and MHC class II molecules; they also exhibited decreased survival associated with acute severe gut GVHD. This rapid-onset, obesity-associated gut GVHD depended on donor CD4+ T cells and occurred even with a minor MHC mismatch between donor and recipient animals. Retrospective analysis of clinical cohorts receiving allo-HSCT transplants from unrelated donors revealed that recipients with a high body mass index (BMI, >30) had reduced survival and higher serum ST2 concentrations compared with nonobese transplant recipients. Assessment of both DIO mice and allo-HSCT recipients with a high BMI revealed reduced gut microbiota diversity and decreased Clostridiaceae abundance. Prophylactic antibiotic treatment protected DIO mouse recipients from endotoxin translocation across the gut and increased inflammatory cytokine production, as well as gut pathology and mortality, but did not protect against later development of chronic skin GVHD. These results suggest that obesity-induced alterations of the gut microbiota may affect GVHD after allo-HSCT in DIO mice, which could be ameliorated by prophylactic antibiotic treatment.

The objective of this study is to describe the clinical features and computed tomography (CT) findings of dogs with retrobulbar disease. There are two facets to this study: a retrospective case series in which findings of dogs with primary vs. secondary retrobulbar disease are described, and a retrospective cross-sectional study in which computed tomography findings of dogs with retrobulbar neoplasia vs. infection/inflammation are described and compared. The medical records of 66 client-owned dogs diagnosed with retrobulbar disease between 2006 and 2016 were reviewed. Clinical information including signalment, the specialty service to which the dog was presented, clinical signs, physical examination findings, diagnostic results, treatment, and outcome were documented. Diagnostic imaging and histopathology were reviewed. Forty-one dogs (62.1%) were diagnosed with primary disease of the retrobulbar space; 25 dogs (37.9%) were considered to have secondary retrobulbar disease. Of the 41 dogs with primary retrobulbar disease, 19 were diagnosed with neoplasia, 19 with infectious/inflammatory disease, and 3 suffered traumatic insult to the retrobulbar space. Of the 25 dogs with secondary retrobulbar disease, 21 were diagnosed with neoplasia, 3 with infectious/inflammatory disease, and 1 with a cyst. Dogs had a combination of ocular, oral, and/or nasal clinical signs. CT findings of orbital osteolysis, orbital periosteal reaction, and presence of a retrobulbar mass were significantly associated with neoplasia, while zygomatic salivary gland enlargement, retrobulbar mass effect, and mandibular lymphadenopathy were more often associated with infectious/inflammatory disease. CT findings overlap among different retrobulbar diseases, but new bone formation and lysis are more often associated with neoplasia. Disease originating from the retrobulbar space was equally likely to be infectious/inflammatory (n = 19) or neoplastic (n = 19), based on definitive diagnostic results of dogs with primary retrobulbar disease. Due to the clinical ramifications of these disorders, the diagnosis and treatment of these cases should be managed with a multi-specialty approach.