CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model.

Current cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored. Due to the over-excess mutations unrelated to cancer, the great challenge is to identify somatic mutations that are cancer-driven. Under the notion that carcinogenesis is a form of somatic-cell evolution, we developed a two-component mixture model: while the ground component corresponds to passenger mutations, the rapidly evolving component corresponds to driver mutations. Then, we implemented an empirical Bayesian procedure to calculate the posterior probability of a site being cancer-driven. Based on these, we developed a software CanDriS (Cancer Driver Sites) to profile the potential cancer-driving sites for thousands of tumor samples from the Cancer Genome Atlas and International Cancer Genome Consortium across tumor types and pan-cancer level. As a result, we identified that approximately 1% of the sites have posterior probabilities larger than 0.90 and listed potential cancer-wide and cancer-specific driver mutations. By comprehensively profiling all potential cancer-driving sites, CanDriS greatly enhances our ability to refine our knowledge of the genetic basis of cancer and might guide clinical medication in the upcoming era of precision medicine. The results were displayed in a database CandrisDB (http://biopharm.zju.edu.cn/candrisdb/).

RHEMITT Score Predicts Rebleed After Capsule Endoscopy: First Validation at a U.S. Tertiary Care Center.

BACKGROUND: Patients with obscure gastrointestinal bleeding undergo small bowel capsule endoscopy (SBCE), but often return for recurrent bleeding or anemia. The RHEMITT score evaluates patients based on 7 variables (heart failure, chronic kidney disease, Saurin P1/P2 lesions, major bleeding, incomplete SBCE, smoking status, and endoscopic treatment) and seeks to predict the risk of rebleeding. AIMS: This study aims to perform an external validation of the RHEMITT score in the United States. METHODS: SBCEs performed to evaluate anemia or GI bleeding from a tertiary-care center's PillCam database between 1/22/2018 and 7/21/2020 were reviewed. Variables based on the RHEMITT score were collected. The primary outcome was rebleeding, defined as (1) melena or hematochezia or (2) hemoglobin drop of 2 g/dL. Patient were categorized into low, intermediate, and high-risk categories based on RHEMITT score. The accuracy of the RHEMITT score for predicting rebleeding was assessed. RESULTS: A total of 361 SBCEs were included in the study. Age, indication for SBCE, endoscopic treatment, antiplatelet use, cirrhosis, heart failure, chronic kidney disease, and major bleeding were significantly associated with risk of rebleed (p < 0.05). Each increasing risk category for the RHEMITT score predicted increased probability of this study's primary outcome, rebleeding (p < 0.001). There was a significant association between RHEMITT risk category and rebleeding-free survival (log-rank p < 0.001). An area under the receiver operating characteristic curve for the RHEMITT score was 0.790 (p < 0.001). CONCLUSION: Our findings validate the RHEMITT score and confirm acceptable performance for predicting rebleeding at a tertiary referral center in the United States.

Liver resection for metastatic GIST tumor improves survival in the era of tyrosine kinase inhibitors: a systematic review and meta-analysis.

INTRODUCTION: Survival for gastrointestinal stromal tumor (GIST) has been increasing over the years after the introduction of tyrosine kinase inhibitors. However, the role of metastasectomy for GIST is still controversial. Patients are currently treated with imatinib or sunitinib in case of imatinib failures as optimal medical therapy for metastatic GIST. METHODS: The Pubmed, EMBASE, and Cochrane Library were systematically searched. Overall survival following liver resection ± tyrosine kinase inhibitor treatment for metastatic GIST was compared to treatment with tyrosine kinase inhibitors alone. RESULTS: Eleven studies including both randomized control trials and retrospective cohort studies were included in the final analysis with a total of 988 patients. Seven studies encompassed data on 556 patients with isolated liver metastases (219 surgery ± drug groups and 337 drug-only groups) were included. Overall survival was significantly improved in patients undergoing liver resection ± drug therapy in comparison to drug therapy alone. [HR (95%CI) = 2.10 (1.58, 2.79); p<0.00001]. Subgroup analysis showed that patients also had improved progression free survival based on 4 studies. [HR (95%CI) = 1.92 (1.43, 2.56); p<0.00001]. In case of concurrent liver and peritoneal metastases, patients showed improved overall survival with aggressive surgical approaches based on 10 studies. [HR (95%CI) = 1.90 (1.56, 2.31); p<0.00001]. CONCLUSION: This meta-analysis found that liver resection for patients with metastatic GIST regardless of peritoneal metastases improved progression free and overall survival in conjunction with tyrosine kinase inhibitors as compared with medical therapy alone. Furthermore, liver resections did not have any immediate detrimental impact on survival in the group of patients selected.

Academic cardiac electrophysiologists' perspectives on sleep apnea care.

PURPOSE: Obstructive sleep apnea syndrome (OSAS) is an important, modifiable risk factor in the pathophysiology of arrhythmias including atrial fibrillation (AF). The purpose of the study was to evaluate cardiac electrophysiologists' (EPs) perception of OSAS. METHODS: We designed a 27-item online Likert scale-based survey instrument entailing several domains: (1) relevance of OSAS in EP practice, (2) OSAS screening and diagnosis, (3) perception on treatments for OSAS, (4) opinion on the OSAS care model. The survey was distributed to 89 academic EP programs in the USA and Canada. While the survey instrument questions refer to the term sleep apnea (SA), our discussion of the diagnosis, management, and research on the sleep disorder is more accurately described with the term OSAS. RESULTS: A total of 105 cardiac electrophysiologists from 49 institutions responded over a 9-month period. The majority of respondents agreed that sleep apnea (SA) is a major concern in their practice (94%). However, 42% reported insufficient education on SA during training. Many (58%) agreed that they would be comfortable managing SA themselves with proper training and education and 66% agreed cardiac electrophysiologists should become more involved in management. Half of EPs (53%) were not satisfied with the sleep specialist referral process. Additionally, a majority (86%) agreed that trained advanced practice providers should be able to assess and manage SA. Time constraints, lack of knowledge, and the referral process are identified as major barriers to EPs becoming more involved in SA care. CONCLUSIONS: We found that OSAS is widely recognized as a major concern for EP. However, incorporation of OSAS care in training and routine practice lags. Barriers to increased involvement include time constraints and education. This study can serve as an impetus for innovation in the cardiology OSAS care model.

A case of Lomentospora prolificans endophthalmitis treated with the novel antifungal agent Olorofim.

PURPOSE: To report a case of endogenous Lomentospora prolificans endophthalmitis treated with the novel antifungal agent Olorofim. CASE REPORT: A 57-year-old man developed disseminated Lomentospora prolificans with right endophthalmitis on the background of immunosuppression following lung transplantation for interstitial lung disease. He was treated with early vitrectomy, intravitreal voriconazole, and systemic Olorofim, voriconazole and terbinafine. His symptoms improved and remained stable in the right eye. Eight weeks later the patient represented with Lomentopora prolificans endophthalmitis in the left eye when systemic voriconazole and terbinafine treatment were withdrawn. Despite aggressive treatment he ultimately succumbed due to vascular complications of extensive disseminated disease. CONCLUSION: We report a rare case of disseminated Lomentosporosis with panophthalmitis in an immunocompromised host with prolonged survival on systemic Olorofim, voriconazole and terbinafine in conjunction with pars plana vitrectomy and intravitreal voriconazole. Early suspicion of an opportunistic fungal infection is critical, as managing disseminated disease is often unsuccessful. Despite presumed inherent resistance, intravitreal and systemic voriconazole appeared to limit disease progression in the right eye. The potential synergistic effects of combined antifungal therapy with orotomides warrant further investigation.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.

Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.

Age-dependent immune and lymphatic responses after spinal cord injury.

Spinal cord injury (SCI) causes lifelong debilitating conditions. Previous works demonstrated the essential role of the immune system in recovery after SCI. Here, we explored the temporal changes of the response after SCI in young and aged mice in order to characterize multiple immune populations within the mammalian spinal cord. We revealed substantial infiltration of myeloid cells to the spinal cord in young animals, accompanied by changes in the activation state of microglia. In contrast, both processes were blunted in aged mice. Interestingly, we discovered the formation of meningeal lymphatic structures above the lesion site, and their role has not been examined after contusive injury. Our transcriptomic data predicted lymphangiogenic signaling between myeloid cells in the spinal cord and lymphatic endothelial cells (LECs) in the meninges after SCI. Together, our findings delineate how aging affects the immune response following SCI and highlight the participation of the spinal cord meninges in supporting vascular repair.

The functional and evolutionary impacts of human-specific deletions in conserved elements.

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel reporter assays in six cell types, we discovered 800 hCONDELs conferring significant differences in regulatory activity, half of which enhance rather than disrupt regulatory function. We highlight several hCONDELs with putative human-specific effects on brain development, including HDAC5, CPEB4, and PPP2CA. Reverting an hCONDEL to the ancestral sequence alters the expression of LOXL2 and developmental genes involved in myelination and synaptic function. Our data provide a rich resource to investigate the evolutionary mechanisms driving new traits in humans and other species.

Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.

Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Leveraging base-pair mammalian constraint to understand genetic variation and human disease.

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Evolutionary constraint and innovation across hundreds of placental mammals.

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth's vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

Robotic pancreaticoduodenectomy provides better histopathological outcomes as compared to its open counterpart: a meta-analysis.

The aim of this meta-analysis was to evaluate whether robotic pancreaticoduodenectomy (PD) may provide better clinical and pathologic outcomes compared to its open counterpart. The Pubmed, EMBASE, and Cochrane Library were systematically searched. Overall postoperative morbidity and resection margin involvement rate were the primary endpoints. Secondary endpoints included operating time, estimated blood loss (EBL), incisional surgical site infection (SSI) rate, length of hospital stay (LOS), and number of lymph nodes harvested. Twenty-four studies totaling 12,579 patients (2,175 robotic PD and 10,404 open PD were included. Overall postoperative mortality did not significantly differ [OR (95%CI) = 0.86 (0.74, 1.01); p = 0.06]. Resection margin involvement rate was significantly lower in robotic PD [15.6% vs. 19.9%; OR (95%CI) = 0.64 (0.41, 1.00); p = 0.05; NNT = 23]. Operating time was significantly longer in robotic PD [MD (95%CI) = 75.17 (48.05, 102.28); p < 0.00001]. EBL was significantly decreased in robotic PD [MD (95%CI) = - 191.35 (- 238.12, - 144.59); p < 0.00001]. Number of lymph nodes harvested was significantly higher in robotic PD [MD (95%CI) = 2.88 (1.12, 4.65); p = 0.001]. This meta-analysis found that robotic PD provides better histopathological outcomes as compared to open PD at the cost of longer operating time. Furthermore, robotic PD did not have any detrimental impact on clinical outcomes, with lower wound infection rates.

Impact of Gender on Transcatheter Aortic Valve Implantation Outcomes.

Previous studies indicate that women who underwentwho underwent transcatheter aortic valve implantation (TAVI) have poorer 30-day outcomes compared with men. However, the effect of gender as a prognostic factor for long-term outcomes following TAVI remains unclear. Between 2008 and 2018, all patients (n = 683) who underwent TAVI in 2 centres in Melbourne, Australia were prospectively included in a registry. The primary end-point was long-term mortality. The secondary end points were Valve Academic Research Consortium-2 (VARC-2) in-hospital complications and mortality at 30-days and 1-year. Of 683 patients, 328 (48%) were women. Women had a higher mean STS-PROM score (5.2 ± 3.1 vs 4.6 ± 3.5, p < 0.001) but less co-morbidities than men. Women had a significantly higher in-hospital bleeding rates (3.3% vs 1.0%, Odds Ratio 4.21, 95% confidence interval [CI] 1.16 to15.25, p = 0.027) and higher 30-day mortality (2.4% vs 0.3%, hazard ratio [HR] 8.75, 95% CI 1.09 to 69.6, p = 0.040) than men. Other VARC-2 outcomes were similar between genders. Overall mortality rate was 36% (246) over a median follow up of 2.7 (interquartile rang [IQR] 1.7 to 4.2) years. Median time to death was 5.3 (95% CI 4.7 to 5.7) years. One-year mortality was similar between genders (8.3% vs 7.8%), as was long-term mortality (HR = 0.91, 95% CI 0.71 to 1.17, p = 0.38). On multivariable analysis, female gender was an independent predictor for 1-year mortality (HR = 2.33, 95% CI 1.11 to 4.92, p = 0.026), but not long-term mortality (HR = 0.78, 95% CI 0.54 to 1.14, p = 0.20). In the women only cohort, STS-PROM was the only independent predictor of long-term mortality (HR 1.88, 95% CI 1.42 to 2.48, p < 0.001). In conclusion, women had higher rates of peri-procedural major bleeding and 30-day mortality following TAVI. However, long-term outcomes were similar between genders.

PBBs, PBDEs, and PCBs levels in hair of residents around e-waste disassembly sites in Zhejiang Province, China, and their potential sources.

This study was conducted to explore the exposure potential of Chinese residents to PBBs, PBDEs, and PCBs in e-waste disassembly sites in Zhejiang province. The contents of 23 PBB congeners, 12 PBDE congeners, and 27 PCB congeners in hair and in their potential sources, including soil and e-waste, were measured via GC-MS. The levels of PHAHs in the three subfamilies (i.e., the PBBs, PBDEs, and PCBs) were all considerably higher (P<0.05) in hair samples collected from the disassembly sites than from the control site. The highest levels of PBBs (57.77 ng g(-1) dw), PBDEs (29.64 ng g(-1) dw), and PCBs (181.99 ng g(-1) dw) in hair were all found in those from the disassembly site Xinqiu, which are respectively 2, 2, and 10 times more than those observed in hair from the control site Yandang. Among the three subfamilies of PHAHs, PCBs were the most predominant pollutants detected. PBBs, which have very limited information available in China, can be detected at a comparable level with PBDEs in these samples in the study. Therefore, these observations suggested that more attention should be given over the potential for environmental or occupational exposure to PHAHs present in e-waste. By and large, the PHAH levels measured in the hair samples were consistent with those detected in the soil. Hair analysis could thus be a valid screening tool for assessing human PHAHs exposure in and around e-waste disassembly sites.

CNS lymphatic drainage and neuroinflammation are regulated by meningeal lymphatic vasculature.

Neuroinflammatory diseases, such as multiple sclerosis, are characterized by invasion of the brain by autoreactive T cells. The mechanism for how T cells acquire their encephalitogenic phenotype and trigger disease remains, however, unclear. The existence of lymphatic vessels in the meninges indicates a relevant link between the CNS and peripheral immune system, perhaps affecting autoimmunity. Here we demonstrate that meningeal lymphatics fulfill two critical criteria: they assist in the drainage of cerebrospinal fluid components and enable immune cells to enter draining lymph nodes in a CCR7-dependent manner. Unlike other tissues, meningeal lymphatic endothelial cells do not undergo expansion during inflammation, and they express a unique transcriptional signature. Notably, the ablation of meningeal lymphatics diminishes pathology and reduces the inflammatory response of brain-reactive T cells during an animal model of multiple sclerosis. Our findings demonstrate that meningeal lymphatics govern inflammatory processes and immune surveillance of the CNS and pose a valuable target for therapeutic intervention.

High resolution reversed phase analysis of recombinant monoclonal antibodies by ultra-high pressure liquid chromatography column coupling.

Monoclonal antibodies (mAbs) represent one of the fastest growing areas of new drug development. However, their analytical characterization is complex and generally requires an array of orthogonal analytical techniques. Reversed phase liquid chromatography is a valuable strategy due to its high resolving power and straightforward compatibility to mass spectrometry. The present study demonstrates that high peak capacity can be attained with intact mAb of ~150 kDa, reduced mAb fragments of ~25-50 kDa and also digested mAb generating numerous peptides of ~0.5-3 kDa. Several long columns packed with fully porous wide-pore sub-2 µm particles were coupled in series to evaluate the effect of column length on peak capacity. By using three columns of 150 mm length, a mobile phase temperature of 80 °C and a gradient time of around 20 min, peak capacities of 117 and 128 were obtained for a commercial intact mAb and its reduced mAb fragments, respectively. On the other hand, when peptide mapping was performed at 50 °C, with a gradient time of 270 min and a column length of 450 mm, a peak capacity of more than 700 was achieved.