Functional genomic landscape of cancer-intrinsic evasion of killing by T cells.

The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood1-3. Here, to identify a phenotypically robust core set of genes and pathways that enable cancer cells to evade killing mediated by cytotoxic T lymphocytes (CTLs), we performed genome-wide CRISPR screens across a panel of genetically diverse mouse cancer cell lines that were cultured in the presence of CTLs. We identify a core set of 182 genes across these mouse cancer models, the individual perturbation of which increases either the sensitivity or the resistance of cancer cells to CTL-mediated toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated manner in which genes and pathways act in cancer cells to orchestrate their evasion of CTLs, and shows that discrete functional modules that control the interferon response and tumour necrosis factor (TNF)-induced cytotoxicity are dominant sub-phenotypes. Our data establish a central role for genes that were previously identified as negative regulators of the type-II interferon response (for example, Ptpn2, Socs1 and Adar1) in mediating CTL evasion, and show that the lipid-droplet-related gene Fitm2 is required for maintaining cell fitness after exposure to interferon-γ (IFNγ). In addition, we identify the autophagy pathway as a conserved mediator of the evasion of CTLs by cancer cells, and show that this pathway is required to resist cytotoxicity induced by the cytokines IFNγ and TNF. Through the mapping of cytokine- and CTL-based genetic interactions, together with in vivo CRISPR screens, we show how the pleiotropic effects of autophagy control cancer-cell-intrinsic evasion of killing by CTLs and we highlight the importance of these effects within the tumour microenvironment. Collectively, these data expand our knowledge of the genetic circuits that are involved in the evasion of the immune system by cancer cells, and highlight genetic interactions that contribute to phenotypes associated with escape from killing by CTLs.

Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells.

Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. In this study, we investigated functional drivers of post-treatment recurrent GBM through integrative genomic analyses, genome-wide genetic perturbation screens in patient-derived GBM models and independent lines of validation. Specific genetic dependencies were found consistent across recurrent tumor models, accompanied by increased mutational burden and differential transcript and protein expression compared to its primary GBM predecessor. Our observations suggest a multi-layered genetic response to drive tumor recurrence and implicate PTP4A2 (protein tyrosine phosphatase 4A2) as a modulator of self-renewal, proliferation and tumorigenicity in recurrent GBM. Genetic perturbation or small-molecule inhibition of PTP4A2 acts through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1) and its downstream molecular players, exploiting a functional dependency on ROBO signaling. Because a pan-PTP4A inhibitor was limited by poor penetrance across the blood-brain barrier in vivo, we engineered a second-generation chimeric antigen receptor (CAR) T cell therapy against ROBO1, a cell surface receptor enriched across recurrent GBM specimens. A single dose of ROBO1-targeted CAR T cells doubled median survival in cell-line-derived xenograft (CDX) models of recurrent GBM. Moreover, in CDX models of adult lung-to-brain metastases and pediatric relapsed medulloblastoma, ROBO1 CAR T cells eradicated tumors in 50-100% of mice. Our study identifies a promising multi-targetable PTP4A-ROBO1 signaling axis that drives tumorigenicity in recurrent GBM, with potential in other malignant brain tumors.

Interrater reliability of a phenotypic assessment tool for the ear morphology in microtia.

The Elements of Morphology Standard Terminology working group published standardized definitions for external ear morphology. The primary objective of our study was to use these descriptions to evaluate the interrater reliability for specific features associated with microtia. We invited six raters from three different subspecialities to rate 100 ear photographs on 32 features. We calculated overall and within specialty and professional experience intraclass correlation coefficients (ICC) and 95% confidence intervals. A total of 600 possible observations were recorded for each feature. The overall interrater reliability ranged from 0.04 (95% CI: 0.00-0.14) for the width of the antihelix inferior crus to 0.93 (95% CI: 0.91-0.95) for the presence of the inferior crux of the antihelix. The reliability for quantitative characteristics such as length or width of an ear structure was generally lower than the reliability for qualitative characteristics (e.g., presence or absence of an ear structure). Categories with very poor interrater reliability included anti-helix inferior crux width (0.04, 95% CI: 0.00-0.14), crux helix extension (0.17, 95% CI 0.00-0.37), and shape of the incisura (0.14, 95% CI: 0.01-0.27). There were no significant differences in reliability estimates by specialty or professional experience for most variables. Our study showed that it is feasible to systematically characterize many of structures of the ear that are affected in microtia. We incorporated these descriptions into a standardized phenotypic assessment tool (PAT-Microtia) that might be used in multicenter research studies to identify sub-phenotypes for future studies of microtia.

Perioperative Acetaminophen and Dexmedetomidine Eliminate Post-Operative Opioid Requirement following Pediatric Tonsillectomy.

Administration of post-operative opioids following pediatric tonsillectomy can elicit respiratory events in this patient population that often arise as central and obstructive sleep apnea. The primary objective of this study was to determine whether a perioperative combination of dexmedetomidine and acetaminophen could eliminate post-operative (in recovery and at home) opioid requirements. Following IRB approval and a waiver for informed consent, the medical records of 681 patients who underwent tonsillectomy between 1 January 2013 and 31 December 2018 were evaluated. Between 1 January 2013 and 31 December 2015, all patients received a fentanyl-sevoflurane-based anesthetic, without acetaminophen or dexmedetomidine, and received opioids in recovery and for discharge home. On 1 January 2016, an institution-wide practice change replaced this protocol with a multimodal perioperative regimen of acetaminophen (intravenous or enteral) and dexmedetomidine and eliminated post-operative opioids. This is the first time that the effect of an acetaminophen and dexmedetomidine combination on the perioperative and home opioid requirement has been reported. Primarily, we compared the need for rescue opioids in the post-anesthesia care period and after discharge. The multi-modal protocol eliminated the need for post-tonsillectomy opioid administration. Dexmedetomidine in combination with acetaminophen eliminated the need for post-operative opioids in the recovery period.

Evidence for diminished levels of epithelial psoriasin and calprotectin in chronic rhinosinusitis.

BACKGROUND: Decreased epithelial expression of mRNA for S100A7 (psoriasin) and S100A8/A9 (calprotectin) has been reported in patients with chronic rhinosinusitis (CRS). OBJECTIVES: We sought to assess whether the expression of S100 proteins is also altered in the sinonasal cavity of patients with CRS. METHODS: We determined levels of S100 proteins in nasal lavage fluid and sinonasal tissue extracts from patients with CRS using ELISA and immunohistochemical analysis of nasal polyp tissue from patients with CRS with nasal polyps and uncinate tissue from healthy control subjects, patients with CRSsNP, and patients with CRSwNP. RESULTS: Expression levels of S100 proteins were decreased compared with those seen in control subjects in nasal lavage fluid from both CRS groups (P < .05). Similarly, tissue expression of these proteins assessed by means of immunohistochemistry demonstrated clear reductions, primarily in the epithelial lining. Interestingly, levels of calprotectin were increased in nasal polyp tissue despite lower levels in lavage fluid. Levels of calprotectin in nasal tissues were correlated with levels of neutrophils, as assessed by means of quantification of neutrophil elastase. CONCLUSIONS: Several S100 proteins are in the epidermal differentiation complex of genes and have been demonstrated to play a role in maintenance of barrier function and formation of an antimicrobial shield. We demonstrate significantly decreased levels of expression of S100 proteins in the epithelium of patients with CRS, which might lead to diminished innate immune responses and barrier function. Increased levels of calprotectin in nasal polyp tissue might reflect neutrophil recruitment and a compensatory mechanism. Future studies will be important to determine whether reduced levels of S100 proteins lead to decreased antimicrobial responses in the upper airways and sinuses and whether this reduction plays a causative role in CRS pathogenesis and susceptibility to infectious disease.

Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2.

STAG2, a component of the mitotically essential cohesin complex, is highly mutated in several different tumour types, including glioblastoma and bladder cancer. Whereas cohesin has roles in many cancer-related pathways, such as chromosome instability, DNA repair and gene expression, the complex nature of cohesin function has made it difficult to determine how STAG2 loss might either promote tumorigenesis or be leveraged therapeutically across divergent cancer types. Here, we have performed whole-genome CRISPR-Cas9 screens for STAG2-dependent genetic interactions in three distinct cellular backgrounds. Surprisingly, STAG1, the paralog of STAG2, was the only negative genetic interaction that was shared across all three backgrounds. We also uncovered a paralogous synthetic lethal mechanism behind a genetic interaction between STAG2 and the iron regulatory gene IREB2 Finally, investigation of an unusually strong context-dependent genetic interaction in HAP1 cells revealed factors that could be important for alleviating cohesin loading stress. Together, our results reveal new facets of STAG2 and cohesin function across a variety of genetic contexts.

Alterations in epithelial barrier function and host defense responses in chronic rhinosinusitis.

Chronic rhinosinusitis (CRS) is characterized by a chronic symptomatic inflammation of the nasal and paranasal sinus mucosae and is one of the most frequently reported chronic diseases in the United States, with an estimated prevalence of greater than 10% of the general population. Although the pathogenesis of CRS remains poorly understood, there is evidence for a role of bacteria and fungi, as well as the presence of a robust adaptive immune response in the upper airways and sinuses. Recent studies of CRS, as well as several other diseases in the skin and respiratory epithelium, have uncovered evidence that deficiencies in epithelial immune barrier function might compromise the interaction between the host and external immune stimuli. Recent studies suggest the hypothesis that reduced expression of antimicrobial S100 proteins, particularly psoriasin and calprotectin, might lead to increased susceptibility to bacterial and fungal colonization in patients with CRS. The main emphasis of this review will be to highlight the current literature that suggests that a defect in the expression of a broad set of epithelially derived genes might lead to barrier compromise and subsequently a dysfunctional host immune response to environmental agents in patients with CRS.

Multisystem Inflammatory Syndrome in Children in a 15-Year-Old Male with a Retropharyngeal Phlegmon.

This is a case of a 15-year-old male with an initial diagnosis of a retropharyngeal phlegmon who ultimately developed new symptoms and laboratory findings consistent with MIS-C. This case report demonstrates an atypical initial presentation for MIS-C that has not been reported in the literature.

Parturient With Barnes Syndrome (Thoracolaryngopelvic Dysplasia) Undergoing Cesarean Delivery of a Neonate With Barnes Syndrome: A Case Report.

This case describes a parturient with Barnes syndrome, a rare disorder characterized by subglottic stenosis, thoracic dystrophy, and small pelvic inlet, who underwent cesarean delivery of a neonate diagnosed with Barnes syndrome. Live simulation training was performed by multidisciplinary team to prepare for the spinal anesthetic, personnel flow between 2 operating rooms, and management of various airway scenarios for the newborn. After delivery, the neonate underwent laryngoscopy-bronchoscopy with successful intubation in the operating room because of labored breathing. Airway evaluation revealed subglottic stenosis, tracheomalacia/bronchomalacia. Collaboration among perinatologists, obstetric/pediatric anesthesiologists, pediatric head and neck surgeons, and neonatologists was integral to perioperative management of both the mother and child.

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens.

The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines.

Expression patterns of Hox10 paralogous genes during lumbar spinal cord development.

We have examined the expression of three paralogous Hox genes from E11.5 through E15.5 in the mouse spinal cord. These ages coincide with major phases of spinal cord neurogenesis, neuronal differentiation, cell migration, gliogenesis, and motor neuron cell death. The three genes, Hoxa10, Hoxc10, and Hoxd10, are all expressed in the lumbar spinal cord and have distinct expression patterns. Mutations in these three genes are known to affect motor neuron patterning. All three genes show lower levels of expression at the rostral limits of their domains, with selective regions of higher expression more caudally. Hoxa10 and Hoxd10 expression appears confined to postmitotic cell populations in the intermediate and ventral gray, while Hoxc10 is also expressed in proliferating cells in the dorsal ventricular zone. Hoxc10 and Hoxd10 expression is clearly excluded from the lateral motor columns at rostral lumbar levels but is present in this region more caudally. Double labeling demonstrates that Hoxc10 expression is correlated with ventrolateral LIM gene expression in the caudal part of the lumbar spinal cord.

Prospective study of perioperative factors predicting hypocalcemia after thyroid and parathyroid surgery.

OBJECTIVE: To identify whether perioperative 1,25-dihydroxyvitamin D or parathyroid hormone (PTH) levels will predict the development of hypocalcemia after thyroid and parathyroid surgery. DESIGN: Prospective study. SETTING: University hospital. PATIENTS: The study included 103 patients who underwent thyroid or parathyroid surgery between 2002 and 2004, with a comparison of the patients who underwent thyroid lobectomy (TL; n = 34), total thyroidectomy (TT; n = 27), parathyroid adenoma excision (PAE; n = 34), and subtotal parathyroidectomy for hyperplasia (SP; n = 8). MAIN OUTCOME MEASURES: Preoperative 1,25-dihydroxyvitamin D levels, number of patients requiring calcium replacement, and postoperative PTH and calcium levels. RESULTS: No patients in the TL or PAE group developed postoperative hypocalcemia that required calcium replacement. Six patients (22%) in the TT group and 3 patients (38%) in the SP group required calcium replacement for clinically significant hypocalcemia (P<.001). All patients who required calcium replacement had PTH levels of less than 15 pg/mL (1.6 pmol/L) 8 hours after surgery. Among the patients with postoperative PTH levels of less than 15 pg/mL (1.6 pmol/L) 8 hours after surgery, no patients in the PAE group required calcium replacement, compared with 75% of patients in the TT and SP groups (P<.001). The patients in the TT group had significantly lower postoperative calcium levels than those in the TL (P<.001) or the PAE (P<.005) group. The patients in the TL group reached stable calcium levels significantly earlier than those in the other groups (15.8 hours after surgery; P<.05). There was no relationship between preoperative 1,25-dihydroxyvitamin D levels and postoperative calcium levels. CONCLUSIONS: Preoperative 1,25-dihydroxyvitamin D levels were not predictive of postoperative calcium levels. Patients who undergo PAE or TL are at extremely low risk for requiring calcium replacement. Patients who undergo TT or SP with 8-hour postoperative PTH levels greater than or equal to 15 pg/mL (1.6 pmol/L) are at low risk for developing postoperative hypocalcemia, whereas those with PTH levels less than 15 pg/mL (1.6 pmol/L) have a high risk of developing hypocalcemia.

Conjunctival T-cell subpopulations in Sjögren's and non-Sjögren's patients with dry eye.

PURPOSE: To examine the conjunctiva of patients with Sjögren's syndrome keratoconjunctivitis sicca (SS-KCS) and non-Sjögren's keratoconjunctivitis sicca (NS-KCS) for evidence of immune-based inflammation. METHODS: Conjunctival biopsy specimens were obtained from 15 patients with SS-KCS and 15 with NS-KCS. Immunohistochemistry was performed on frozen sections to characterize and quantify T-cell subtypes (CD3, CD4, and CD8) and markers of immune activation (major histocompatibility complex [MHC] class II: HLA-DR, HLA-DQ) and inflammation (intercellular adhesion molecule [ICAM]-1). The numbers of cells positive for each marker were counted by two masked observers and averaged. RESULTS: Conjunctival biopsy specimens from patients with SS-KCS or NS-KCS revealed lymphocytic infiltration and increased immunoreactivity for the markers of inflammation and immune activation. The extent of cellular immunoreactivity did not differ significantly between SS-KCS and NS-KCS tissue samples. CONCLUSIONS: The authors' findings indicate that patients with SS-KCS or NS-KCS have conjunctival inflammation manifested by inflammatory cell infiltrates and upregulation of expression in markers of immune activation. Clinical symptoms of KCS may be more dependent on T-cell activation and resultant inflammation than previously believed. In addition to tear substitutes, anti-inflammatory therapeutics should be investigated for the treatment of KCS.

Complementary and integrative treatments: swallowing disorders.

Swallowing disorders are associated with many disease processes and are associated with significant morbidity and mortality. This article provides information regarding the various causes of swallowing disorders as well as medical, surgical, and integrative approaches to their management.

Single-stage excision of localized head and neck venous malformations using preoperative glue embolization.

OBJECTIVE: Describe single-stage removal of head and neck venous malformations using percutaneous embolization with n-butyl cyanoacrylate (n-BCA) glue prior to surgical resection. STUDY DESIGN: Case series with chart review. SETTING: Tertiary-care pediatric hospital. SUBJECTS AND RESULTS: A total of 169 venous malformations were identified between 2000 and 2012, and 102 (60.1%) were in the head and neck. Thirty-five of 102 (34.3%) were observed, 56 of 102 (54.9%) had invasive therapy, and 11 of 102 (10.8%) underwent n-BCA embolization and surgery ("GES procedure"). The median age of the glue embolization and surgery cohort was 14 years (range, 6-19), and 7 of 11 (63.6%) were female. Treated venous malformations involved the oral cavity/tongue (4/11; 36.4%) and parotid/face (7/11; 63.6%). During facial lesion excision, intraoperative facial nerve monitoring was used. All surgical sites (11/11) were closed primarily. No patient in this cohort had any posttreatment nerve deficits, dysarthria, and dysphagia or lesion persistence. CONCLUSIONS: Localized venous malformations can be treated with preoperative percutaneous embolization with n-BCA glue followed by surgical excision. This technique, with selective motor nerve monitoring, appears safe and allows for complete venous malformation removal with limited nerve dissection, to allow maximal tissue and functional preservation.

Generation of consensus in the application of a rating scale to nasendoscopic assessment of velopharyngeal function.

OBJECTIVE: To generate consensus ratings of velopharyngeal function on nasendoscopy (NE) with the goal of creating a video instruction tool. METHODS: The American Society of Pediatric Otolaryngology Velopharyngeal Insufficiency Study Group convened to identify NE segments to be included in an instructional video. Of 24 segments reviewed, 11 were selected based on the quality of the examinations and spectrum of closure patterns. Participating otolaryngologists independently rated NE segments using the Golding-Kushner scale. The participants then convened and rated each of the NE segments as a group. Thirty-nine members of the American Society of Pediatric Otolaryngology met and agreed with the group ratings, creating a consensus standard. RESULTS: Individual scores for palate and lateral wall motion showed high variability, ranging from 0 to 6 points difference from the consensus. Variability was also seen for the following qualitative findings: the Passavant ridge, aberrant pulsations, and dorsal palatal notch. The individual ratings are presented graphically to demonstrate the range of individual responses as well as to compare responses to the consensus ratings. No further changes were made to the proposed consensus ratings when reviewed by the larger group. CONCLUSIONS: Rating of NE evaluations of velopharyngeal function was variable among a group of pediatric otolaryngologists experienced in treating velopharyngeal insufficiency. These results highlight the need to develop a standardized method of reporting NE findings for velopharyngeal insufficiency. Despite this, consensus ratings were achieved that will facilitate development of a video instruction tool.

ICAM-1 expression predisposes ocular tissues to immune-based inflammation in dry eye patients and Sjögrens syndrome-like MRL/lpr mice.

PURPOSE: We previously reported that immune-based inflammation occurs on the ocular surface of humans as well as canines with keratoconjunctivitis sicca (KCS). Intercellular adhesion molecule-1 (ICAM-1) was found to be upregulated on lymphocytes and/or vascular endothelial cells resulting in lymphocytic diapedesis to the lacrimal and conjunctival tissues. The purpose of the current study was to demonstrate the role of ICAM-1 in (1) resident epithelial cell response during ocular inflammation, (2) local and/or peripheral lymphocyte activation or accumulation in the ocular tissues, and (3) whether anti-ICAM-1 is effective to attenuate immune-mediated ocular inflammation. METHODS: ICAM-1 levels in various ocular tissues of human with KCS and/or MRL/lpr mouse were evaluated by immunohistochemistry and in situ hybridization for protein and messenger RNA (mRNA) expression, respectively. Soluble ICAM-1 concentrations in MRL/lpr mouse plasma over the course of disease development were measured by ELISA. Cell proliferation within ocular tissues was assessed by bromodeoxyuridine (BrdU) incorporation and immunohistochemical detection. The level of T cell activation was determined by IL-2 receptor (CD25, a marker of T cell activation and proliferation) and CD69 (a marker of T cell activation) immunoreactivity using FACS analysis. To examine the effectiveness of anti-ICAM-1/LFA-1 in elimination of lacrimal gland inflammation, MRL/lpr mice were injected intraperitoneally (i.p.) with or without monoclonal antibodies against ICAM-1 and LFA-1 at three or eight weeks of age. RESULTS: Increased endogenous ICAM-1 expression at the level of protein and mRNA was detected in the epithelial cells present in the conjunctival and accessory lacrimal tissues in dry eye patients. In MRL/lpr mice, ICAM-1 expression by lacrimal acinar epithelial cells and conjunctival epithelial cells were detected in addition to inflammatory infiltrates and vascular endothelial cells at 16 weeks of age. Soluble ICAM-1 levels were markedly increased concomitantly with disease progression over time as compared with the controls. No significant lymphocytic proliferation (a lack of BrdU and CD25 immunoreactivities) was detected within lacrimal glands of MRL/lpr mice at the disease onset. However, a population of the infiltrated T cells were CD69 positive, indicating the activation stage of a T cell subset. Treatment using monoclonal antibodies against murine ICAM-1 and LFA-1 resulted in a decrease in the number of inflammatory infiltrates in MRL/lpr mice. CONCLUSIONS: Our findings suggest that ICAM-1 upregulation locally and systemically promote lymphocyte activation and migration to the ocular surface (OS). Ocular resident epithelium is an active component of ocular surface and is capable of interacting with invasive lymphocytes by ICAM-1 production in response to immune activation and inflammation. ICAM-1 synthesized by epithelial cells may serve as a signaling molecule for predisposition of ocular surface inflammation and facilitate potential antigen presentation by epithelial cells. Lymphocytic infiltrates in the lacrimal gland of the MRL/lpr mouse appeared to be the result of the accumulation, but not proliferation of circulating lymphocytes diapodesed from the vasculature that had migrated into the local ocular tissues. The potential use of anti-ICAM-1 therapy in treating immune-based inflammatory diseases such as dry eye deserves further investigation.