Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale.

Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.

A degron-based approach to manipulate Eomes functions in the context of the developing mouse embryo.

The T-box transcription factor Eomesodermin (Eomes), also known as Tbr2, plays essential roles in the early mouse embryo. Loss-of-function mutant embryos arrest at implantation due to Eomes requirements in the trophectoderm cell lineage. Slightly later, expression in the visceral endoderm promotes anterior visceral endoderm formation and anterior-posterior axis specification. Early induction in the epiblast beginning at day 6 is necessary for nascent mesoderm to undergo epithelial to mesenchymal transition (EMT). Eomes acts in a temporally and spatially restricted manner to sequentially specify the yolk sac haemogenic endothelium, cardiac mesoderm, definitive endoderm, and axial mesoderm progenitors during gastrulation. Little is known about the underlying molecular mechanisms governing Eomes actions during the formation of these distinct progenitor cell populations. Here, we introduced a degron-tag and mCherry reporter sequence into the Eomes locus. Our experiments analyzing homozygously tagged embryonic stem cells and embryos demonstrate that the degron-tagged Eomes protein is fully functional. dTAG (degradation fusion tag) treatment in vitro results in rapid protein degradation and recapitulates the Eomes-null phenotype. However in utero administration of dTAG resulted in variable and lineage-specific degradation, likely reflecting diverse cell type-specific Eomes expression dynamics. Finally, we demonstrate that Eomes protein rapidly recovers following dTAG wash-out in vitro. The ability to temporally manipulate Eomes protein expression in combination with cell marking by the mCherry-reporter offers a powerful tool for dissecting Eomes-dependent functional roles in these diverse cell types in the early embryo.

The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors.

Extra-embryonic mesoderm (ExM)-composed of the earliest cells that traverse the primitive streak-gives rise to the endothelium as well as haematopoietic progenitors in the developing yolk sac. How a specific subset of ExM becomes committed to a haematopoietic fate remains unclear. Here we demonstrate using an embryonic stem cell model that transient expression of the T-box transcription factor Eomesodermin (Eomes) governs haemogenic competency of ExM. Eomes regulates the accessibility of enhancers that the transcription factor stem cell leukaemia (SCL) normally utilizes to specify primitive erythrocytes and is essential for the normal development of Runx1+ haemogenic endothelium. Single-cell RNA sequencing suggests that Eomes loss of function profoundly blocks the formation of blood progenitors but not specification of Flk-1+ haematoendothelial progenitors. Our findings place Eomes at the top of the transcriptional hierarchy regulating early blood formation and suggest that haemogenic competence is endowed earlier during embryonic development than was previously appreciated.

Inhibition of Pannexin 1 Reduces the Tumorigenic Properties of Human Melanoma Cells.

Pannexin 1 (PANX1) is a channel-forming glycoprotein expressed in many tissues including the skin. PANX1 channels allow the passage of ions and molecules up to 1 kDa, including ATP and other metabolites. In this study, we show that PANX1 is highly expressed in human melanoma tumors at all stages of disease progression, as well as in patient-derived cells and established melanoma cell lines. Reducing PANX1 protein levels using shRNA or inhibiting channel function with the channel blockers, carbenoxolone (CBX) and probenecid (PBN), significantly decreased cell growth and migration, and increased melanin production in A375-P and A375-MA2 cell lines. Further, treatment of A375-MA2 tumors in chicken embryo xenografts with CBX or PBN significantly reduced melanoma tumor weight and invasiveness. Blocking PANX1 channels with PBN reduced ATP release in A375-P cells, suggesting a potential role for PANX1 in purinergic signaling of melanoma cells. In addition, cell-surface biotinylation assays indicate that there is an intracellular pool of PANX1 in melanoma cells. PANX1 likely modulates signaling through the Wnt/ß-catenin pathway, because ß-catenin levels were significantly decreased upon PANX1 silencing. Collectively, our findings identify a role for PANX1 in controlling growth and tumorigenic properties of melanoma cells contributing to signaling pathways that modulate melanoma progression.

Patterns, perceptions, and perceived barriers to physical activity in adult cancer survivors.

PURPOSE: Physical activity (PA) during and after cancer treatment is associated with improved cancer- and non-cancer-related outcomes. We assessed for predictors of change in PA levels among cancer survivors. METHODS: Adult cancer survivors from a comprehensive cancer center completed a one-time questionnaire retrospectively assessing PA levels before, during, and after cancer treatment along with their perceptions of PA. Multivariable logistic regression models evaluated the association of clinico-demographics variables and perceptions of PA with changes in whether patients were meeting PA guidelines after cancer diagnosis. RESULTS: Among the 1003 patients, 319 (32%) met moderate to vigorous PA (MVPA) guidelines before diagnosis. Among those meeting guidelines before diagnosis, 50% still met guidelines after treatment; 12% not meeting MVPA guidelines initially met them after treatment/at follow-up. Among patients meeting guidelines before diagnosis, better ECOG performance status at follow-up, receiving curative therapy, and spending a longer time on PA initially were each associated with meeting guidelines at follow-up. After controlling for other variables, perceiving that PA improves quality of life (adjusted odds ratio, aOR = 11.09, 95%CI [1.42-86.64], P = 0.02) and overall survival (aOR = 8.52, 95%CI [1.12-64.71], P = 0.04) was each associated with meeting MVPA guidelines during/after treatment, in patients who did not meet guidelines initially. Only 13% reported receiving counseling, which was not associated with PA levels. Common reported barriers to PA included fatigue, lacking motivation, and being too busy. CONCLUSIONS: Patient perceptions of PA benefits are strongly associated with improving PA levels after a cancer diagnosis. Clinician counseling should focus on patient education and changing patient perceptions.

Cancer patients' acceptability of incorporating an epidemiology questionnaire within a clinical trial.

BACKGROUND/AIMS: Understanding the influence or impact of epidemiological factors on cancer outcomes in clinical trials can broaden our knowledge of disease, trial populations and therapeutic effects thus leading to improved patient care. However, there is a lack of data on cancer patients' compliance with an epidemiology questionnaire in the context of a clinical trial. PATIENTS AND METHODS: Cancer patients were provided with a hypothetical scenario and surveyed regarding their willingness and preferences to complete an epidemiology questionnaire if incorporated into a cancer therapy trial. Patient compliance with completing a voluntary epidemiology questionnaire and trial coordinators perceptions therein were separately determined in the NCIC Clinical Trials Group HN.6 clinical trial, an ongoing randomized phase III trial comparing two first-line treatment regimens in patients with locoregionally advanced head and neck cancer. RESULTS: Of 617 cancer patients from community, academic and tertiary cancer centres, the majority were willing to complete an epidemiology questionnaire either unconditionally (45%), or provided it did not inconvenience them (31%); 4% would refuse. Patients preferred shorter questionnaires of 30-50 questions requiring 10-20 min to complete, administered over 1-3 sessions. Patients were less willing, but still compliant, to answer questions relating to sexual history (71%) and annual household income (66%) relative to other questions (>90%). Eighteen percent thought that the questionnaire should be mandatory, with 31% believing that they may benefit personally from such research. In the HN.6 trial, compliance averaged 94.8% per question. CONCLUSIONS: Cancer patients are very willing to complete epidemiology questions in clinical trials.

Pannexin channels and their links to human disease.

In less than a decade, a small family of channel-forming glycoproteins, named pannexins, have captured the interest of many biologists, in large part due to their association with common diseases, ranging from cancers to neuropathies to infectious diseases. Although the pannexin family consists of only three members (Panx1, Panx2 and Panx3), one or more of these pannexins are expressed in virtually every mammalian organ, implicating their potential role in a diverse array of pathophysiologies. Panx1 is the most extensively studied, but features of this pannexin must be cautiously extrapolated to the other pannexins, as for example we now know that Panx2, unlike Panx1, exhibits unique properties such as a tendency to be retained within intracellular compartments. In the present review, we assess the biochemical and channel features of pannexins focusing on the literature which links these unique molecules to over a dozen diseases and syndromes. Although no germ-line mutations in genes encoding pannexins have been linked to any diseases, many cases have shown that high pannexin expression is associated with disease onset and/or progression. Disease may also occur, however, when pannexins are underexpressed, highlighting that pannexin expression must be exquisitely regulated. Finally, we discuss some of the most pressing questions and controversies in the pannexin field as the community seeks to uncover the full biological relevance of pannexins in healthy organs and during disease.

Second-hand smoke as a predictor of smoking cessation among lung cancer survivors.

PURPOSE: Second-hand smoke (SHS; ie, exposure to smoking of friends and spouses in the household) reduces the likelihood of smoking cessation in noncancer populations. We assessed whether SHS is associated with cessation rates in lung cancer survivors. PATIENTS AND METHODS: Patients with lung cancer were recruited from Princess Margaret Cancer Centre, Toronto, ON, Canada. Multivariable logistic regression and Cox proportional hazard models evaluated the association of sociodemographics, clinicopathologic variables, and SHS with either smoking cessation or time to quitting. RESULTS: In all, 721 patients completed baseline and follow-up questionnaires with a mean follow-up time of 54 months. Of the 242 current smokers at diagnosis, 136 (56%) had quit 1 year after diagnosis. Exposure to smoking at home (adjusted odds ratio [aOR], 6.18; 95% CI, 2.83 to 13.5; P < .001), spousal smoking (aOR, 6.01; 95% CI, 2.63 to 13.8; P < .001), and peer smoking (aOR, 2.49; 95% CI, 1.33 to 4.66; P = .0043) were each associated with decreased rates of cessation. Individuals exposed to smoking in all three settings had the lowest chances of quitting (aOR, 9.57; 95% CI, 2.50 to 36.64; P < .001). Results were similar in time-to-quitting analysis, in which 68% of patients who eventually quit did so within 6 months after cancer diagnosis. Subgroup analysis revealed similar associations across early- and late-stage patients and between sexes. CONCLUSION: SHS is an important factor associated with smoking cessation in lung cancer survivors of all stages and should be a key consideration when developing smoking cessation programs for patients with lung cancer.

Comorbidity and prognosis in head and neck cancers: Differences by subsite, stage, and human papillomavirus status.

BACKGROUND: The prognostic utility of comorbidity on head and neck cancer may differ by subsite, stage, and human papillomavirus (HPV) status. METHODS: We reviewed the medical records of 4953 patients with head and neck cancer for comorbidity (Charlson Comorbidity Index [CCI]), smoking, and alcohol history. Multivariate proportional hazards assessed the association of CCI with survival. HPV status was determined using p16 immunohistochemistry. RESULTS: After accounting for stage, higher CCI was associated with worse overall survival (OS) in nasopharyngeal (hazard ratio [HR], 2.93; 95% confidence interval [CI], 1.53-5.62), oropharyngeal (HR, 1.99; 95% CI, 1.63-2.43), and oral cavity cancers (HR, 1.54; 95% CI, 1.27-1.86). These associations were most prominent in the early stage oral cavity (HR, 2.11; 95% CI, 1.50-2.96) and laryngeal (HR, 1.87; 95% CI, 1.35-2.58) cancers, and in advanced stage oropharyngeal (HR, 2.23; 95% CI, 1.81-2.74) and nasopharyngeal (HR, 3.50; 95% CI, 1.76-6.97) cancers. CCI was independently prognostic even in the HPV-adjusted oropharyngeal cancers. CONCLUSION: Comorbidity was prognostic in subsets of nasopharyngeal, oropharyngeal, oral cavity, and laryngeal cancers. Comorbidity may be a partial surrogate for age and social habits.

The changing incidence of human papillomavirus-associated oropharyngeal cancer using multiple imputation from 2000 to 2010 at a Comprehensive Cancer Centre.

INTRODUCTION: Human papillomavirus (HPV) is a risk and prognostic factor for oropharyngeal cancer (OPC). Determining whether the incidence of HPV-associated OPC is rising informs health policy. METHODS: HPV status was ascribed using p16 immunohistochemistry in 683/1474 OPC patients identified from the Princess Margaret Hospital's Cancer Registry (from 2000 to 2010). Missing p16 data was estimated using multiple (n=100) imputation (MI) and validated using an independent OPC cohort (n=214). Non-OPC head and neck squamous cell carcinoma (HNSCC) (n=3262) were also used for time-trend comparison. Regression was used to compare HNSCC subsets and time-trends. The c-index was used to measure the predictive ability of MI. RESULTS: The incidence of OPC rose from 23.3% of all HNSCC in 2000 to 31.2% in 2010 (p=0.002). In the subset of OPC tested for p16, there was no change in p16 positivity over time (p=0.9). However, p16 testing became more frequent over time (p<0.0001), but was nonetheless biased, favouring never-smokers [OR 1.87 (95% CI 1.29-2.70)] and tumors of the tonsil [OR 2.30 (1.52-3.47)] or base-of-tongue [OR 1.72 (1.10-2.70)]. These same factors were also associated with p16-positivity [ORs 3.22 (1.27-8.16), 7.26 (3.50-15.1), 5.83 (2.70-12.7), respectively]. Following MI and normalization, the proportion of OPC that was p16-associated rose from 39.8% in 2000 to 65.0% in 2010, p=0.002, fully explaining the rise in OPC in our patient population. CONCLUSION: The rise in HNSCC referrals seen from 2000 to 2010 at our institution was driven primarily by p16-associated OPC. MI was necessary to derive reliable conclusions when cases with missing data are considerable.

Validation of a one-page patient-reported Charlson comorbidity index questionnaire for upper aerodigestive tract cancer patients.

OBJECTIVES: Cancer patients have a wide range of comorbidities that are important confounders for biomarker and clinical studies of prognosis and outcome. Comorbidities can be captured using the Charlson Comorbidity Index (CCI) through abstraction of medical records, but patient-reported outcome (PRO) questionnaires have also been used. The objective was to validate the PRO-CCI in a head and neck cancer (HNC) population, and to assess its level of agreement with the standard (std-CCI) method of chart review. METHODS: A one-page PRO-CCI was compared with the std-CCI obtained through independent abstraction in 882 HNC patients (2007-2010). Kappa statistics and associated measures (p(pos) and p(neg)) were used to assess agreement. Discrepancy for each comorbid illness was evaluated. Proportional hazard models compared the association of std-CCI and PRO-CCI with overall survival (OS). Adjustments were made and a modified PRO-CCI was re-evaluated in a new cohort of upper aerodigestive tract cancers patient. RESULTS: PRO-CCI was higher than the std-CCI (p < 0.0001). After adjustment, having at least two comorbidities according to either the std-CCI [HR 1.97 (1.38-2.80)] or the PRO-CCI [HR 1.62 (1.18-2.24)] was prognostic. Of the most prevalent comorbidities, agreement was high for most of the CCI elements (kappa 0.76-0.93), but poorest agreement for connective tissue disease (kappa = 0.29, p(pos) = 43%, p(neg) = 84%) and COPD (kappa = 0.48, p(pos) = 53%, p(neg) = 95%). When the connective tissue disease question was modified, agreement of this item improved (kappa = 0.47, p(pos) = 50%). CONCLUSION: PRO-CCI can be an easy and effective tool in prognostic and outcomes research in HNC patients.