Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.

DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.

The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated RNAP mechanism, and RNAP mutations drive Escherichia coli adaptation to many health- and industry-relevant environments, yet a paucity of systematic analyses hampers our understanding of the fitness trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and prevent killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships in vivo and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.

Atezolizumab for Advanced Alveolar Soft Part Sarcoma.

BACKGROUND: Alveolar soft part sarcoma (ASPS) is a rare soft-tissue sarcoma with a poor prognosis and no established therapy. Recently, encouraging responses to immune checkpoint inhibitors have been reported. METHODS: We conducted an investigator-initiated, multicenter, single-group, phase 2 study of the anti-programmed death ligand 1 (PD-L1) agent atezolizumab in adult and pediatric patients with advanced ASPS. Atezolizumab was administered intravenously at a dose of 1200 mg (in patients ≥18 years of age) or 15 mg per kilogram of body weight with a 1200-mg cap (in patients <18 years of age) once every 21 days. Study end points included objective response, duration of response, and progression-free survival according to Response Evaluation Criteria in Solid Tumors (RECIST), version 1.1, as well as pharmacodynamic biomarkers of multistep drug action. RESULTS: A total of 52 patients were evaluated. An objective response was observed in 19 of 52 patients (37%), with 1 complete response and 18 partial responses. The median time to response was 3.6 months (range, 2.1 to 19.1), the median duration of response was 24.7 months (range, 4.1 to 55.8), and the median progression-free survival was 20.8 months. Seven patients took a treatment break after 2 years of treatment, and their responses were maintained through the data-cutoff date. No treatment-related grade 4 or 5 adverse events were recorded. Responses were noted despite variable baseline expression of programmed death 1 and PD-L1. CONCLUSIONS: Atezolizumab was effective at inducing sustained responses in approximately one third of patients with advanced ASPS. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT03141684.).

Outcomes of Femoral Popliteal Bypass in Octogenarians.

INTRODUCTION: Femoral-popliteal bypass (FPB) surgery is a common lower extremity revascularization procedure. As the population continues to age, this procedure is being performed increasingly on older patients. This study investigated whether outcomes differ in this population. MATERIALS AND METHODS: Patients over and less than 80 years old who underwent FPB between 2009-2013 were queried using an existing hospital registry. Demographics, comorbidities, intraoperative complications, perioperative outcomes, and two-year patencies were compared. RESULTS: Twenty-four patients in the octogenarian cohort (OC) and 72 patients in the non-octogenarian cohort (NOC) were identified. There was a lower prevalence of smoking (p=0.018) and higher prevalence of hypertension (p=0.021) among octogenarians. Other medical characteristics were similar (p<0.05). There were no differences in use of vein versus PTFE (p=0.002) as a conduit, or above (OC 20.0% vs. NOC 36.7%), versus below knee (OC 80.0% vs. NOC 63.3%) distal anastomosis (p>0.05) between the groups. There was a difference (p<0.01) in indication for procedure (OC/NOC): claudication (0%/44%), limb salvage (71%/31%), and rest pain (29%/25%). There were no differences in 30-day readmissions (17% vs. 21%; p=0.59) or incidence of postoperative (25% vs. 19%; p=0.56) or intraoperative complications (8.3% vs. 4.2%; p=0.52). Length of stay (LOS) was longer and statistically significant in octogenarians (12 days vs. 7 days; p=0.032) and remained significant after multivariate linear regression (p=0.015). Patencies in OC were lower and dropped faster after six months; however, there were no statistically significant differences in patencies at any time interval (p>0.05). The position of the distal anastomosis relative to the knee, conduit type, and indication were not independently predictive of patency outcomes (p>0.05). CONCLUSION: The safety and efficacy of FPB in octogenarians is similar to the general population despite LOS in octogenarians being 5.98 days longer. While the difference in indication suggests that vascular surgeons are more conservative in treating octogenarians, our analysis did not reveal significant differences between populations and suggests that lower extremity bypass can be performed safely with comparable results in this cohort. A larger cohort is needed to validate these results.

Operative Management of Acute Appendicitis Was Safe During the COVID-19 Pandemic Shutdown.

INTRODUCTION: In the spring of 2020, New York City was one of the first epicenters of the COVID outbreak. In this study, we evaluate the incidence and treatment of appendicitis in two New York City community hospitals during the COVID pandemic. METHODS: This retrospective study focused on the incidence and outcome of acute appendicitis in the adult population (>18 y old) during peak-COVID periods (March 16, 2020,-June 15, 2020) compared to pre-COVID and post-COVID periods. We compared the number of patients who underwent operative versus nonoperative management, patient demographics, length of stay (LOS), complications, and readmission rates within these time periods. Data are presented as mean ± standard deviation (analysis of variance). RESULTS: From January 1, 2020 to December 31, 2020, 393 patients presented with acute appendicitis and 321 (81.7%) were treated operatively, compared to 441 total and 366 treated operatively (83%) in 2019 (P = 0.88). During the COVID outbreak, fewer patients presented with appendicitis (mean 6.9 ± 1 pre-COVID case/week, 4.4 ± 2.4 peak-COVID cases/week and 7.6 ± 0.65 post-COVID cases/week, P = 0.018) with no significant difference in the pre-COVID and post-COVID period. There was no difference in LOS between the pre-, peak-, and post-COVID periods with a median of 1 for all the three, (interquartile range (IQR): 0.8-2, 0.6-2, 0.6-2, respectively, P = 0.43). Additionally, there was no difference in 30-day readmission rates (4.2%, 0%, 3.9%, P = 0.99) and postoperative complications (4.2%, 0%, 2.9%, P = 0.98). CONCLUSIONS: During peak-COVID, there was a significant reduction in the number of patients who presented with acute appendicitis without a post rebound increase in presentation. Those who presented during peak-COVID were able to undergo operative management safely, without affecting LOS or postoperative complications.

Case Volume Justification of 3D-Navigated Spinal Procedures: A Cost-Benefit Analysis.

3D image-guidance platforms have transformed spinal surgery by enhancing visualization, increasing precision, and improving patient outcomes. However, with high procurement, operational, and maintenance costs relative to the standard of care, the benefits of acquiring these platforms must be thoroughly assessed. This study aims to develop a model that weighs the cost of a typical 3D navigation platform against its clinical benefits to determine the facility case volume required to justify its purchase. Using Medtronic's StealthStation and O-Arm as a market example, we calculated the break-even case volume by dividing the cost of the platform by the difference in gross margins between 3D navigation and the standard of care. Total gross margins earned from first-time and revision surgeries were calculated based on each payer's reimbursement rate and covered case volume, as well as each technology's revision rate. Values reported in literature and by Centers for Medicare and Medicaid Services databases were plugged into the model to calculate variables. At a 0% reimbursement rate from private payers for revision surgeries, an annual case volume of 158 spinal surgeries would be required to justify the per-year 3D navigation cost; at 100% private payer reimbursement, 352 surgeries would be required. Given these volumes, 61% of all US inpatient facilities cannot justify 3D navigation at 0% reimbursement, and 86% cannot justify it at 100% reimbursement. Accordingly, greater pricing flexibility, such as per-procedure models, is required for 3D navigation systems to standardize clinical outcomes across medical centers.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5,000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a 10-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills.

Defining the role of neoadjuvant systemic therapy in high-risk retroperitoneal sarcoma: A multi-institutional study from the Transatlantic Australasian Retroperitoneal Sarcoma Working Group.

BACKGROUND: In patients with retroperitoneal sarcoma (RPS), the incidence of recurrence after surgery remains high. Novel treatment approaches are needed. This retrospective study evaluated patients with primary, high-risk RPS who received neoadjuvant systemic therapy followed by surgery to 1) determine the frequency and potential predictors of radiologic tumor responses and 2) assess clinical outcomes. METHODS: Clinicopathologic data were collected for eligible patients treated at 13 sarcoma referral centers from 2008 to 2018. Univariable and multivariable logistic models were performed to assess the association between clinical predictors and response. Overall survival (OS) and crude cumulative incidences of local recurrence and distant metastasis were compared. RESULTS: Data on 158 patients were analyzed. A median of 3 cycles of neoadjuvant systemic therapy (interquartile range, 2-4 cycles) were given. The regimens were mostly anthracycline based; however, there was significant heterogeneity. No patients demonstrated a complete response, 37 (23%) demonstrated a partial response (PR), 88 (56%) demonstrated stable disease, and 33 (21%) demonstrated progressive disease (PD) according to the Response Evaluation Criteria in Solid Tumors, version 1.1. Only a higher number of cycles given was positively associated with PR (P = .005). All patients underwent complete resection, regardless of the tumor response. Overall, patients whose tumors demonstrated PD before surgery showed markedly worse OS (P = .005). An indication of a better clinical outcome was seen in specific regimens given for grade 3 dedifferentiated liposarcoma and leiomyosarcoma. CONCLUSIONS: In patients with high-risk RPS, the response to neoadjuvant systemic therapy is fair overall. Disease progression on therapy may be used to predict survival after surgery. Subtype-specific regimens should be further validated.

Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation.

In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.

Screening for distress and needs: Findings from a multinational validation of the Adolescent and Young Adult Psycho-Oncology Screening Tool with newly diagnosed patients.

OBJECTIVE: Adolescents and young adults (AYAs) diagnosed with cancer commonly experience elevated psychological distress and need appropriate detection and management of the psychosocial impact of their illness and treatment. This paper describes the multinational validation of the Distress Thermometer (DT) for AYAs recently diagnosed with cancer and the relationship between distress and patient concerns on the AYA-Needs Assessment (AYA-NA). METHODS: AYA patients (N = 288; 15-29 years, Mage  = 21.5 years, SDage  = 3.8) from Australia (n = 111), Canada (n = 67), the UK (n = 85) and the USA (n = 25) completed the DT, AYA-NA, Hospital Anxiety Depression Scale (HADS) and demographic measures within 3 months of diagnosis. Using the HADS as a criterion, receiver operating characteristics analysis was used to determine the optimal cut-off score and meet the acceptable level of 0.70 for sensitivity and specificity. Correlations between the DT and HADS scores, prevalence of distress and AYA-NA scores were reported. RESULTS: The DT correlated strongly with the HADS-Total, providing construct validity evidence (r = 0.65, p < 0.001). A score of 5 resulted in the best clinical screening cut-off on the DT (sensitivity = 82%, specificity = 75%, Youden Index = 0.57). Forty-two percent of AYAs scored at or above 5. 'Loss of meaning or purpose' was the AYA-NA item most likely to differentiate distressed AYAs. CONCLUSIONS: The DT is a valid distress screening instrument for AYAs with cancer. The AYA-POST (DT and AYA-NA) provides clinicians with a critical tool to assess the psychosocial well-being of this group, allowing for the provision of personalised support and care responsive to individuals' specific needs and concerns.

Operative Shutdown and Recovery: Restructuring Surgical Operations During the SARS-CoV-2 Pandemic.

BACKGROUND: During the 2020 SARS-CoV-2 outbreak in New York City, hospitals canceled elective surgeries to increase capacity for critically ill patients. We present case volume data from our community hospital to demonstrate how this shutdown affected surgical care. METHODS: Between March 16 and June 14, 2020, all elective surgeries were canceled at our institution. All procedures performed during this operating room shutdown (ORS) were logged, as well as those 4 weeks before (PRE) and 4 weeks after (POST) for comparison. RESULTS: A total of 2,475 cases were included in our analysis, with 754 occurring during shutdown. Overall case numbers dropped significantly during ORS and increased during recovery (mean 245.0 ± 28.4 PRE versus 58.0 ± 30.9 ORS versus 186.0±19.4 POST cases/wk, P< 0.001). Emergency cases predominated during ORS (26.4% PRE versus 59.3% ORS versus 31.5% POST, P< 0.001) despite decreasing in frequency (mean 64.5 ± 7.9 PRE versus 34.4 ± 12.1 ORS versus 58.5 ± 4.0 POST cases/wk, P< 0.001). Open surgeries remained constant in all three phases (52.2-54.1%), whereas laparoscopic and robotic surgeries decreased (-3.4% and -3.0%, P< 0.001). General and/or vascular surgery, urology, and neurosurgery comprised a greater proportion of caseload (+9.5%, +3.0%, +2.8%), whereas orthopedics, gynecology, and otolaryngology/plastic surgery all decreased proportionally (-5.0%, -4.4%, -5.9%, P< 0.001). CONCLUSION: Operative volume significantly decreased during the SARS-CoV-2 outbreak. Emergency cases predominated during this time, although there were fewer emergency cases overall. General/vascular surgery became the most active service and open surgeries became more common. This reallocation of resources may be useful for future crisis planning among community hospitals.

ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

The Evidence and Conclusion Ontology (ECO) contains terms (classes) that describe types of evidence and assertion methods. ECO terms are used in the process of biocuration to capture the evidence that supports biological assertions (e.g. gene product X has function Y as supported by evidence Z). Capture of this information allows tracking of annotation provenance, establishment of quality control measures and query of evidence. ECO contains over 1500 terms and is in use by many leading biological resources including the Gene Ontology, UniProt and several model organism databases. ECO is continually being expanded and revised based on the needs of the biocuration community. The ontology is freely available for download from GitHub (https://github.com/evidenceontology/) or the project's website (http://evidenceontology.org/). Users can request new terms or changes to existing terms through the project's GitHub site. ECO is released into the public domain under CC0 1.0 Universal.

Large-bore Aspiration Thrombectomy for Acute Venous Thromboembolism.

Pulmonary embolism can occur following dislodgement of deep venous thrombosis into the pulmonary artery circulation, which results in obstruction of the pulmonary artery system and can be fatal. The consequences of pulmonary embolism include hypotension, right heart strain, and hypoxia. In the long term, pulmonary embolism may lead to Chronic Thromboembolic Pulmonary Hypertension (CTEPH). Patients who develop hypotensive massive and submassive pulmonary embolism can be treated with large-bore aspiration thrombectomy. In the acute setting, this improves short-term outcomes by decreasing the ICU stay. It can also reduce the risk of CTEPH. Options for large-bore aspiration thrombectomy include the FlowTriever™ system (Inari Medical, Irvine, CA) and the Lightning 12 vascular thrombectomy system (Penumbra Inc., Alameda, CA). This review discusses the pathophysiology of pulmonary embolism, management, and options for large-bore aspiration thrombectomy.

Transcarotid Artery Revascularization and Advances in Vascular Surgery for Carotid Artery Disease.

Carotid artery atherosclerotic disease impacts over 2 million Americans annually. Since the advent of the carotid endarterectomy by Debakey in 1953, the surgical management of carotid artery stenosis has prevented cerebrovascular accidents. The technology utilized to manage carotid artery stenosis continued to evolve with the utilization of carotid artery stenting in 1989 and more recently transcarotid artery revascularization (TCAR). This review discusses the modern management of carotid artery stenosis with an emphasis on transcarotid artery revascularization (TCAR) and reversal of flow for reversal of flow for embolic protection.

Predictors of readmission after craniotomy for meningioma resection: a nationwide readmission database analysis.

BACKGROUND: Meningiomas are the most common benign primary brain tumors. The mainstay of treatment, surgical resection, is often curative. Given the excellent prognosis of these lesions, minimizing perioperative complications is of the utmost importance. With the establishment of the National Readmissions Database (NRD), researchers are now able to identify variables associated with postoperative complications beyond the index admission. OBJECTIVE: In this study, we sought to identify the leading causes for non-elective readmission and variables associated with increased likelihood of readmission at 30 and 90 days after discharge following a craniotomy for meningioma resection. METHODS: Adult inpatients who underwent craniotomy for meningioma resection between 2010 and 2014 were queried from the NRD. All-cause readmissions following craniotomy at 30 and 90 days were identified, and a multivariable logistic regression model was used to characterize independent risk factors. RESULTS: Among 26,034 patients who received craniotomy for meningioma resection, 2825 (10.9%) were readmitted at 30 days and 3436 (16.1%) were readmitted at 90 days. Postoperative wound infection was the most common readmission diagnosis, occurring in 9.32% and 10.2% of 30- and 90-day readmissions respectively. Patient factors associated with increased likelihood of readmission included male gender, greater illness severity, non-routine discharge, index length of hospitalization, and having Medicare or Medicaid insurance. CONCLUSIONS: Readmission following craniotomy for meningioma resection occurs at a clinically significant rate. Several patient factors were identified in association with all-cause 30- and 90-day readmissions. Further studies are required to identify means for preventing complications following discharge in these vulnerable patient populations.

Potent and rapid activation of tropomyosin-receptor kinase A in endometrial stromal fibroblasts by seminal plasma.

Seminal plasma (SP), the liquid fraction of semen, is not mandatory for conception, but clinical studies suggest that SP improves implantation rates. Prior in vitro studies examining the effects of SP on the endometrium, the site of implantation, surprisingly revealed that SP induces transcriptional profiles associated with neurogenesis. We investigated the presence and activity of neurogenesis pathways in the endometrium, focusing on TrkA, one of the canonical receptors associated with neurotrophic signaling. We demonstrate that TrkA is expressed in the endometrium. To determine if SP activates TrkA signaling, we isolated the two most abundant endometrial cell types-endometrial epithelial cells (eEC) and endometrial stromal fibroblasts (eSF)-and examined TrkA activity in these cells after SP exposure. While SP only moderately activated TrkA in eEC, it potently and rapidly activated TrkA in eSF. This activation occurred in both non-decidualized and decidualized eSF. Blocking this pathway resulted in dysregulation of SP-induced cytokine production by eSF. Surprisingly, while the canonical TrkA agonist nerve growth factor was detected in SP, TrkA activation was principally induced by a 30-100-kDa protein whose identity remains to be established. Our results show that TrkA signaling is highly active in eSF and is rapidly induced by SP.

An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli.

With the wide availability of whole-genome sequencing (WGS), genetic mapping has become the rate-limiting step, inhibiting unbiased forward genetics in even the most tractable model organisms. We introduce a rapid deconvolution resource and method for untagged causative mutations after mutagenesis, screens, and WGS in Escherichia coli. We created Deconvoluter-ordered libraries with selectable insertions every 50 kb in the E. coli genome. The Deconvoluter method uses these for replacement of untagged mutations in the genome using a phage-P1-based gene-replacement strategy. We validate the Deconvoluter resource by deconvolution of 17 of 17 phenotype-altering mutations from a screen of N-ethyl-N-nitrosourea-induced mutants. The Deconvoluter resource permits rapid unbiased screens and gene/function identification and will enable exploration of functions of essential genes and undiscovered genes/sites/alleles not represented in existing deletion collections. This resource for unbiased forward-genetic screens with mapping-by-sequencing ('forward genomics') demonstrates a strategy that could similarly enable rapid screens in many other microbes.

Pembrolizumab in advanced soft-tissue sarcoma and bone sarcoma (SARC028): a multicentre, two-cohort, single-arm, open-label, phase 2 trial.

BACKGROUND: Patients with advanced sarcomas have a poor prognosis and few treatment options that improve overall survival. Chemotherapy and targeted therapies offer short-lived disease control. We assessed pembrolizumab, an anti-PD-1 antibody, for safety and activity in patients with advanced soft-tissue sarcoma or bone sarcoma. METHODS: In this two-cohort, single-arm, open-label, phase 2 study, we enrolled patients with soft-tissue sarcoma or bone sarcoma from 12 academic centres in the USA that were members of the Sarcoma Alliance for Research through Collaboration (SARC). Patients with soft-tissue sarcoma had to be aged 18 years or older to enrol; patients with bone sarcoma could enrol if they were aged 12 years or older. Patients had histological evidence of metastatic or surgically unresectable locally advanced sarcoma, had received up to three previous lines of systemic anticancer therapy, had at least one measurable lesion according to the Response Evaluation Criteria In Solid Tumors version 1.1, and had at least one lesion accessible for biopsy. All patients were treated with 200 mg intravenous pembrolizumab every 3 weeks. The primary endpoint was investigator-assessed objective response. Patients who received at least one dose of pembrolizumab were included in the safety analysis and patients who progressed or reached at least one scan assessment were included in the activity analysis. Accrual is ongoing in some disease cohorts. This trial is registered with ClinicalTrials.gov, number NCT02301039. FINDINGS: Between March 13, 2015, and Feb 18, 2016, we enrolled 86 patients, 84 of whom received pembrolizumab (42 in each disease cohort) and 80 of whom were evaluable for response (40 in each disease cohort). Median follow-up was 17·8 months (IQR 12·3-19·3). Seven (18%) of 40 patients with soft-tissue sarcoma had an objective response, including four (40%) of ten patients with undifferentiated pleomorphic sarcoma, two (20%) of ten patients with liposarcoma, and one (10%) of ten patients with synovial sarcoma. No patients with leiomyosarcoma (n=10) had an objective response. Two (5%) of 40 patients with bone sarcoma had an objective response, including one (5%) of 22 patients with osteosarcoma and one (20%) of five patients with chondrosarcoma. None of the 13 patients with Ewing's sarcoma had an objective response. The most frequent grade 3 or worse adverse events were anaemia (six [14%]), decreased lymphocyte count (five [12%]), prolonged activated partial thromboplastin time (four [10%]), and decreased platelet count (three [7%]) in the bone sarcoma group, and anaemia, decreased lymphocyte count, and prolonged activated partial thromboplastin time in the soft-tissue sarcoma group (three [7%] each). Nine (11%) patients (five [12%] in the bone sarcoma group and four [10%] in the soft-tissue sarcoma group) had treatment-emergent serious adverse events (SAEs), five of whom had immune-related SAEs, including two with adrenal insufficiency, two with pneumonitis, and one with nephritis. INTERPRETATION: The primary endpoint of overall response was not met for either cohort. However, pembrolizumab showed encouraging activity in patients with undifferentiated pleomorphic sarcoma or dedifferentiated liposarcoma. Enrolment to expanded cohorts of those subtypes is ongoing to confirm and characterise the activity of pembrolizumab. FUNDING: Merck, SARC, Sarcoma Foundation of America, QuadW Foundation, Pittsburgh Cure Sarcoma, and Ewan McGregor.

Bevacizumab alone or in combination with TRC105 for patients with refractory metastatic renal cell cancer.

BACKGROUND: Targeting the vascular endothelial growth factor (VEGF) pathway has improved outcomes in metastatic renal cell carcinoma (RCC); however, resistance inevitably occurs. CD105 (endoglin) is an angiogenic pathway that is strongly upregulated after VEGF inhibition, potentially contributing to resistance. The authors tested whether TRC105, a monoclonal antibody against endoglin, impacted disease control in patients with previously treated RCC who were receiving bevacizumab. METHODS: Eligible patients with metastatic RCC who had previously received 1 to 4 prior lines of therapy, including VEGF-targeted agents, were randomized 1:1 to receive bevacizumab 10 mg/kg intravenously every 2 weeks (arm A) or the same plus TRC105 10 mg/kg intravenously every 2 weeks (arm B). The primary endpoint was progression-free survival (PFS) at 12 and 24 weeks. Correlative studies included serum transforming growth factor ß (TGFß) and CD105 levels as well as tissue immunostaining for TGFß receptors. RESULTS: Fifty-nine patients were enrolled (28 on arm A and 31 on arm B), and 1 patient on each arm had a confirmed partial response. The median PFS for bevacizumab alone was 4.6 months compared with 2.8 for bevacizumab plus TRC105 (P = .09). Grade ≥ 3 toxicities occurred in 16 patients (57%) who received bevacizumab compared with 19 (61%) who received bevacizumab plus TRC105 (P = .9). Baseline serum TGFß levels below the median (<10.6 ng/mL) were associated with longer median PFS (5.6 vs 2.1 months; P = .014). CONCLUSIONS: TRC105 failed to improve PFS when added to bevacizumab. TGFß warrants further study as a biomarker in RCC. Cancer 2017;123:4566-4573. © 2017 American Cancer Society.

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

PortEco (http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating information from a variety of sources. The main focus of PortEco is to enable broad use of the growing number of high-throughput experiments available for E. coli, and to leverage community annotation through the EcoliWiki and GONUTS systems. Currently, PortEco includes curated data from hundreds of genome-wide RNA expression studies, from high-throughput phenotyping of single-gene knockouts under hundreds of annotated conditions, from chromatin immunoprecipitation experiments for tens of different DNA-binding factors and from ribosome profiling experiments that yield insights into protein expression. Conditions have been annotated with a consistent vocabulary, and data have been consistently normalized to enable users to find, compare and interpret relevant experiments. PortEco includes tools for data analysis, including clustering, enrichment analysis and exploration via genome browsers. PortEco search and data analysis tools are extensively linked to the curated gene, metabolic pathway and regulation content at its sister site, EcoCyc.