Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs.

BACKGROUND: About 20% of breast cancers in humans are basal-like, a subtype that is often triple-negative and difficult to treat. An effective translational model for basal-like breast cancer is currently lacking and urgently needed. To determine whether spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. METHODS: We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We identified feature genes for human BLBC and luminal A subtypes via machine learning and used these genes to repeat canine-alone and cross-species tumor classifications. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. RESULTS: Our independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 and feature gene classifications, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched in histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-γ response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors and with the expression of T cell exhaustion markers (e.g., PDCD1) in ER-PR+ canine tumors. CONCLUSIONS: We identify a canine mammary tumor subtype that molecularly resembles human BLBC overall and thus could serve as a vital translational model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.

Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs.

Background: About 20% of breast cancers in humans are basal-like, a subtype that is often triple negative and difficult to treat. An effective translational model for basal-like breast cancer (BLBC) is currently lacking and urgently needed. To determine if spontaneous mammary tumors in pet dogs could meet this need, we subtyped canine mammary tumors and evaluated the dog-human molecular homology at the subtype level. Methods: We subtyped 236 canine mammary tumors from 3 studies by applying various subtyping strategies on their RNA-seq data. We then performed PAM50 classification with canine tumors alone, as well as with canine tumors combined with human breast tumors. We investigated differential gene expression, signature gene set enrichment, expression association, mutational landscape, and other features for dog-human subtype comparison. Results: Our independent genome-wide subtyping consistently identified two molecularly distinct subtypes among the canine tumors. One subtype is mostly basal-like and clusters with human BLBC in cross-species PAM50 classification, while the other subtype does not cluster with any human breast cancer subtype. Furthermore, the canine basal-like subtype recaptures key molecular features (e.g., cell cycle gene upregulation, TP53 mutation) and gene expression patterns that characterize human BLBC. It is enriched histological subtypes that match human breast cancer, unlike the other canine subtype. However, about 33% of canine basal-like tumors are estrogen receptor negative (ER-) and progesterone receptor positive (PR+), which is rare in human breast cancer. Further analysis reveals that these ER-PR+ canine tumors harbor additional basal-like features, including upregulation of genes of interferon-γ response and of the Wnt-pluripotency pathway. Interestingly, we observed an association of PGR expression with gene silencing in all canine tumors, and with the expression of T cell exhaustion markers (e.g., PDCD1 ) in ER-PR+ canine tumors. Conclusions: We identify a canine mammary tumor subtype that molecularly resembles human BLBC overall, and thus could serve as a vital spontaneous animal model of this devastating breast cancer subtype. Our study also sheds light on the dog-human difference in the mammary tumor histology and the hormonal cycle.

Development and internal validation of risk scores to diagnose infectious mononucleosis among college students.

BACKGROUND: Individual symptoms and signs of infectious mononucleosis (IM) are of limited value for diagnosis. OBJECTIVE: To develop and validate risk scores based on signs and symptoms with and without haematologic parameters for the diagnosis of IM. DESIGN AND SETTING: Data were extracted from electronic health records of a university health centre and were divided into derivation (9/1/2015-10/31/2017) and a prospective temporal internal validation (11/1/2017-1/31/2019) cohort. METHOD: Independent predictors for the diagnosis of IM were identified in univariate analysis using the derivation cohort. Logistic regression models were used to develop 2 risk scores: 1 with only symptoms and signs (IM-NoLab) and 1 adding haematologic parameters (IM-Lab). Point scores were created based on the regression coefficients, and patients were grouped into risk groups. Primary outcomes were area under the receiver operating characteristic curve (AUROCC) and classification accuracy. RESULTS: The IM-NoLab model had 4 predictors and identified a low-risk group (7.9% with IM) and a high-risk group (22.2%) in the validation cohort. The AUROCC was 0.75 in the derivation cohort and 0.69 in the validation cohort. The IM-Lab model had 3 predictors and identified a low-risk group (3.6%), a moderate-risk group (12.5%), and a high-risk group (87.6%). The AUROCC was 0.97 in the derivation cohort and 0.93 in the validation cohort. CONCLUSION: We derived and internally validated the IM-NoLab and IM-Lab risk scores. The IM-Lab score in particular had very good discrimination and have the potential to reduce the need for diagnostic testing for IM.

Access and Utilization of Asthma Medications Among Patients Who Receive Care in Federally Qualified Health Centers.

OBJECTIVES: To describe access to and use of prescription asthma medications, and to assess factors associated with asthma exacerbation, healthcare utilization, and health status among asthma patients treated at Federally Qualified Health Centers. METHODS: This is a retrospective cross-sectional study. We analyzed data from the 2014 National Health Center Patient Survey. This data is publicly available from the Health Resources and Services Administration. Data was collected from patients receiving face-to-face care from health centers funded under Section 330 of the Public Health Service Act. Data from patients was collected between October 8, 2014, and April 17, 2015. We included adult participants who reported having a diagnosis of asthma and confirmed that they still have asthma. Association between explanatory variables (access to prescription medications and use of asthma controller medications) and outcome variables (asthma exacerbations, asthma hospitalizations or emergency department visits, and self-rated health) was assessed using multivariable regression analyses while adjusting for demographics. RESULTS: A total of 919 participants with asthma were included. Approximately 32% of the participants experienced delays in getting prescription medications, 26% were unable to get them, 60% experienced an asthma exacerbation last year, 48% rated their health as fair/poor, and 19% visited a hospital or an emergency department last year. Multivariable results showed that participants who were currently taking controller medications were more likely to have experienced an asthma exacerbation (OR = 4.02; 95% CI 1.91 to 8.45; P < .01), or visited a hospital or an emergency department (OR = 3.07; 95% CI 1.39 to 6.73; P < .01) in the last year compared with those who had never taken controller medications. Experiencing difficulties in accessing asthma medications was associated with lower self-rated health (ß = -.51; 95% CI -0.94 to -0.08; P = .02). CONCLUSIONS: Future interventions should seek to improve asthma patient care and health outcomes using innovative strategies that act at multiple levels of the healthcare system (eg, individual, interpersonal, community levels).

Sample size methods for evaluation of predictive biomarkers.

Treatment selection biomarkers are those that can be useful in guiding choice of therapy. Just as new therapies require evaluation in appropriately designed clinical trials to determine their benefit, therapy selection biomarkers require evaluation in appropriately designed studies. These studies may be prospective clinical trials or retrospective studies based on specimens stored from a completed clinical trial. Ideally, patient treatment assignments should be randomized, and consideration should be given to an appropriate sample size-either for prospective planning of a new study or access to a sufficient number of stored specimens. Here, we develop a novel sample size method for estimation of a confidence interval of specified average width, for an intuitively appealing previously proposed parameter that reflects the expected benefit of using biomarker-guided therapy relative to a standard-of-care therapy. The estimation approach combines Monte Carlo and regression to result in a procedure that performs well over a range of scenarios. Although derived under a specific Cox proportional hazards regression model, robustness to model violations is demonstrated by evaluation under accelerated failure time and cure models. The sample size method produces adequate or conservative sample size estimates under a range of scenarios. Computer code in R and C++, and applications for Mac and Windows are made available for implementation of the sample size estimation procedure. The method is applied to a real data setting and results discussed.

Characterization of the Proportion of Clustered Tuberculosis Cases in Guatemala: Insights from a Molecular Epidemiology Study, 2010-2014.

There is little information about the amount of recent tuberculosis transmission in low-income settings. Genetic clustering can help identify ongoing transmission events. A retrospective observational study was performed on Mycobacterium tuberculosis isolates from persons living with HIV (PLHIV) and HIV-seronegative participants who submitted samples to a referral tuberculosis laboratory in Guatemala City, Guatemala from 2010 to 2014. Genotyping results were classified according to the international spoligotyping database, SITVIT2. Spoligotype patterns were categorized as clustered or nonclustered depending on their genotype. The proportion of clustering and the index of recent transmission index (RTIn-1) were estimated. In the RTIn-1 method, clustered cases represent recent transmission, whereas nonclustered cases represent reactivation of older tuberculosis infections. As a secondary aim, the potential risk factors associated with clustering in isolates from the subset of participants living with HIV were explored. From 2010 to 2014, a total of 479 study participants were confirmed as culture-positive tuberculosis cases. Among the 400 available isolates, 71 spoligotype patterns were identified. Overall, the most frequent spoligotyping families were Latin American-Mediterranean (LAM) (39%), followed by T (22%) and Haarlem (14%). Out of the 400 isolates, 365 were grouped in 36 clusters (range of cluster size: 2-92). Thus, the proportion of clustering was 91% and the RTIn-1 was 82%. Among PLHIV, pulmonary tuberculosis was associated with clustering (OR = 4.3, 95% CI 1.0-17.7). Our findings suggest high levels of ongoing transmission of M. tuberculosis in Guatemala as revealed by the high proportion of isolates falling into genomic clusters.

Evaluating biomarkers for treatment selection from reproducibility studies.

We consider evaluating new or more accurately measured predictive biomarkers for treatment selection based on a previous clinical trial involving standard biomarkers. Instead of rerunning the clinical trial with the new biomarkers, we propose a more efficient approach which requires only either conducting a reproducibility study in which the new biomarkers and standard biomarkers are both measured on a set of patient samples, or adopting replicated measures of the error-contaminated standard biomarkers in the original study. This approach is easier to conduct and much less expensive than studies that require new samples from patients randomized to the intervention. In addition, it makes it possible to perform the estimation of the clinical performance quickly, since there will be no requirement to wait for events to occur as would be the case with prospective validation. The treatment selection is assessed via a working model, but the proposed estimator of the mean restricted lifetime is valid even if the working model is misspecified. The proposed approach is assessed through simulation studies and applied to a cancer study.

Canine tumor mutational burden is correlated with TP53 mutation across tumor types and breeds.

Spontaneous canine cancers are valuable but relatively understudied and underutilized models. To enhance their usage, we reanalyze whole exome and genome sequencing data published for 684 cases of >7 common tumor types and >35 breeds, with rigorous quality control and breed validation. Our results indicate that canine tumor alteration landscape is tumor type-dependent, but likely breed-independent. Each tumor type harbors major pathway alterations also found in its human counterpart (e.g., PI3K in mammary tumor and p53 in osteosarcoma). Mammary tumor and glioma have lower tumor mutational burden (TMB) (median < 0.5 mutations per Mb), whereas oral melanoma, osteosarcoma and hemangiosarcoma have higher TMB (median ≥ 1 mutations per Mb). Across tumor types and breeds, TMB is associated with mutation of TP53 but not PIK3CA, the most mutated genes. Golden Retrievers harbor a TMB-associated and osteosarcoma-enriched mutation signature. Here, we provide a snapshot of canine mutations across major tumor types and breeds.

Time to blood, respiratory and urine culture positivity in the intensive care unit: Implications for de-escalation.

OBJECTIVES: Concern for late detection of bacterial pathogens is a barrier to early de-escalation efforts. The purpose of this study was to assess blood, respiratory and urine culture results at 72 h to test the hypothesis that early negative culture results have a clinically meaningful negative predictive value. METHODS: We retrospectively reviewed all patients admitted to the medical intensive care unit between March 2012 and July 2018 with blood cultures obtained. Blood, respiratory and urine culture results were assessed for time to positivity, defined as the time between culture collection and preliminary species identification. The primary outcome was the negative predictive value of negative blood culture results at 72 h. Secondary outcomes included sensitivity, specificity, positive predictive value and negative predictive value of blood, respiratory and urine culture results. RESULTS: The analysis included 1567 blood, 514 respiratory and 1059 urine cultures. Of the blood, respiratory and urine cultures ultimately positive, 90.3%, 76.2% and 90.4% were positive at 72 h. The negative predictive value of negative 72-h blood, respiratory and urine cultures were 0.99, 0.82 and 0.97, respectively. Antibiotic de-escalation had good specificity, positive predictive value and negative predictive value for finalized negative cultures. CONCLUSION: Negative blood and urine culture results at 72 h had a high negative predictive value. These findings have important ramifications for antimicrobial stewardship efforts and support protocolized re-evaluation of empiric antibiotic therapy at 72 h. Caution should be used in patients with clinically suspected pneumonia, since negative respiratory culture results at 72 h were weakly predictive of finalized negative cultures.

Using a Mobile Health Intervention (DOT Selfie) With Transfer of Social Bundle Incentives to Increase Treatment Adherence in Tuberculosis Patients in Uganda: Protocol for a Randomized Controlled Trial.

BACKGROUND: The World Health Organization's End TB Strategy envisions a world free of tuberculosis (TB)-free of deaths, disease, and suffering due to TB-by 2035. Nonadherence reduces cure rates, prolongs infectiousness, and contributes to the emergence of multidrug-resistant TB (MDR-TB). Moreover, MDR-TB is a growing, complex, and costly problem that presents a major obstacle to TB control. Directly observed therapy (DOT) for treatment adherence monitoring is the recommended standard; however, it is challenging to implement at scale because it is labor-intensive. Mobile health interventions can facilitate remote adherence monitoring and minimize the costs and inconveniences associated with standard DOT. OBJECTIVE: The study aims to evaluate the effectiveness of using video directly observed therapy (VDOT) plus incentives to improve medication adherence in TB treatment versus usual-care DOT in an African context. METHODS: The DOT Selfie study is an open-label, randomized controlled trial (RCT) with 2 parallel groups, in which 144 adult patients with TB aged 18-65 years will be randomly assigned to receive the usual-care DOT monitoring or VDOT as the intervention. The intervention will consist of a smartphone app, a weekly internet subscription, translated text message reminders, and incentives for those who adhere. The participant will use a smartphone to record and send time-stamped encrypted videos showing their daily medication ingestion. This video component will directly substitute the need for daily face-to-face meetings between the health provider and patients. We hypothesize that the VDOT intervention will be more effective because it allows patients to swallow their pills anywhere, anytime. Moreover, patients will receive mobile-phone-based "social bundle" incentives to motivate adherence to continued daily submission of videos to the health system. The health providers will log into a secured computer system to verify treatment adherence, document missed doses, investigate the reasons for missed doses, and follow prespecified protocol measures to re-establish medication adherence. The primary endpoint is the adherence level as measured by the fraction of expected doses observed over the treatment period. The main secondary outcome will be time-to-treatment completion in both groups. RESULTS: This study was funded in 2019. Enrollment began in July and is expected to be completed by November 2020. Data collection and follow-up are expected to be completed by June 2021. Results from the analyses based on the primary endpoint are expected to be submitted for publication by December 2021. CONCLUSIONS: This random control trial will be among the first to evaluate the effectiveness of VDOT within an African setting. The results will provide robust scientific evidence on the implementation and adoption of mobile health (mHealth) tools, coupled with incentives to motivate TB medication adherence. If successful, VDOT will apply to other low-income settings and a range of chronic diseases with lifelong treatment, such as HIV/AIDs. TRIAL REGISTRATION: ClinicalTrials.gov NCT04134689; http://clinicaltrials.gov/ct2/show/NCT04134689. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/18029.

Defining adequate contact for transmission of Mycobacterium tuberculosis in an African urban environment.

BACKGROUND: The risk of infection from respiratory pathogens increases according to the contact rate between the infectious case and susceptible contact, but the definition of adequate contact for transmission is not standard. In this study we aimed to identify factors that can explain the level of contact between tuberculosis cases and their social networks in an African urban environment. METHODS: This was a cross-sectional study conducted in Kampala, Uganda from 2013 to 2017. We carried out an exploratory factor analysis (EFA) in social network data from tuberculosis cases and their contacts. We evaluated the factorability of the data to EFA using the Kaiser-Meyer-Olkin Measure of Sampling Adequacy (KMO). We used principal axis factoring with oblique rotation to extract and rotate the factors, then we calculated factor scores for each using the weighted sum scores method. We assessed construct validity of the factors by associating the factors with other variables related to social mixing. RESULTS: Tuberculosis cases (N = 120) listed their encounters with 1154 members of their social networks. Two factors were identified, the first named "Setting" captured 61% of the variance whereas the second, named 'Relationship' captured 21%. Median scores for the setting and relationship factors were 10.2 (IQR 7.0, 13.6) and 7.7 (IQR 6.4, 10.1) respectively. Setting and Relationship scores varied according to the age, gender, and nature of the relationship among tuberculosis cases and their contacts. Family members had a higher median setting score (13.8, IQR 11.6, 15.7) than non-family members (7.2, IQR 6.2, 9.4). The median relationship score in family members (9.9, IQR 7.6, 11.5) was also higher than in non-family members (6.9, IQR 5.6, 8.1). For both factors, household contacts had higher scores than extra-household contacts (p < .0001). Contacts of male cases had a lower setting score as opposed to contacts of female cases. In contrast, contacts of male and female cases had similar relationship scores. CONCLUSIONS: In this large cross-sectional study from an urban African setting, we identified two factors that can assess adequate contact between tuberculosis cases and their social network members. These findings also confirm the complexity and heterogeneity of social mixing.

Video directly observed therapy for supporting and monitoring adherence to tuberculosis treatment in Uganda: a pilot cohort study.

INTRODUCTION: Nonadherence to treatment remains an obstacle to tuberculosis (TB) control worldwide. The aim of this study was to evaluate the feasibility of using video directly observed therapy (VDOT) for supporting TB treatment adherence in Uganda. METHODS: From May to December 2018, we conducted a pilot cohort study at a TB clinic in Kampala City. We enrolled patients aged 18-65 years with ≥3 months remaining of their TB treatment. Participants were trained to use a smartphone app to record videos of medication intake and submit them to a secured system. Trained health workers logged into the system to watch the submitted videos. The primary outcome was adherence measured as the fraction of expected doses observed (FEDO). In a secondary analysis, we examined differences in FEDO by sex, age, phone ownership, duration of follow-up, reasons for missed videos and patients' satisfaction at study exit. RESULTS: Of 52 patients enrolled, 50 were analysed. 28 (56%) were male, the mean age was 31 years (range 19-50 years) and 35 (70%) owned smartphones. Of the 5150 videos expected, 4231 (82.2%) were received. The median FEDO was 85% (interquartile range 66%-94%) and this significantly differed by follow-up duration. Phone malfunction, uncharged battery and VDOT app malfunctions were the commonest reasons for missed videos. 92% of patients reported being very satisfied with using VDOT. CONCLUSION: VDOT was feasible and acceptable for monitoring and supporting TB treatment. It resulted in high levels of adherence, suggesting that digital technology holds promise in improving patient monitoring in Uganda.

Diet-regulated behavior: FVB/N mice fed a lean diet exhibit increased nocturnal bouts of aggression between littermates.

The hyperactive FVB/N inbred mouse strain is widely used for transgenic research applications, although rarely for behavioral studies. These mice have visual impairments via retinal degeneration, but are considered highly intelligent and rely largely on olfaction. While investigating diet-induced obesity in autotaxin transgenic FVB/N mice, we observed an increase in the necessity for male, but not female, cage separations. Based on the observations, we hypothesized that feeding FVB/N mice a lean diet increases nocturnal bouts of aggression between male littermates. The diets of adult littermates were switched from normal chow to either ad libitum high-fat (45% fat) or lean (10% fat) matched diets for 27 weeks, whereby the mice reached an average of 43 g versus 35 g, respectively. Then, cage separations due to nocturnal bouts of aggression became mandatory, even though littermates peacefully cohabitated for 10-16 weeks previously. Since the data was of an unusual nature, it required uncommon statistical methods to be engendered to evaluate whether and where significance existed. Therefore, utilizing the randomization and population models, we established a methodology and postulated that either testosterone, the autotaxin transgene or diet alteration was the causal factor. Statistical evaluation demonstrated a significant correlation between cage separations and aggressive behavior associated with the lean-diet-fed mice, not autotaxin. Biochemical data did not appear to explain the behavior. In contrast, energy metabolism highlighted differences between the groups of normally hyperactive mice by diet. This characteristic makes FVB/N male mice unsuitable subjects for long-term studies with lean-diet modifications.

Impact of a Rapid Point of Care Test for Influenza on Guideline Consistent Care and Antibiotic Use.

BACKGROUND: Rapid influenza diagnostic tests that detect the presence of viral antigens are currently used throughout the United States but have poor sensitivity. The objective of this study was to identify if the use of a new highly accurate rapid point of care test would significantly increase the likelihood of guideline consistent care. METHODS: We prospectively recruited 300 students at a university health clinic who presented with cough and 1 influenza-like illness symptom between December 2016 and February 2017 to receive care guided by a rapid polymerase chain reaction (PCR) test. Of the 300 patients receiving the PCR test, 264 had complete medical records and were compared to 771 who received usual care. We used a logistic regression model to identify whether PCR guided care was associated with guideline consistent care, based on the appropriate use of oseltamivir and antibiotics. We also assessed whether PCR guided care decreased the likelihood of return visits within 2 weeks by patients. RESULTS: Logistic regression revealed that the odds of receiving guideline supported care did not significantly increase for patients who received PCR guided care (adjusted odds ratio [aOR], 1.24; 95% CI, 0.83-1.88). It significantly decreased the likelihood of an antibiotic prescription (aOR, 0.61; 95% CI, 0.40-0.94), increased the likelihood of receiving oseltamivir (aOR, 1.57; 95% CI, 1.09-2.28), and decreased the likelihood of return visit within 2 weeks (aOR, 0.19; 95% CI, 0.04-0.81). CONCLUSIONS: The use of a rapid PCR test did not significantly improve the likelihood of guideline consistent care. However, independent of test outcome, patients who received the test were more likely to receive an antiviral and less likely to receive an antibiotic or have a return visit within 2 weeks.

Urban-rural disparities in treatment outcomes among recurrent TB cases in Southern Province, Zambia.

BACKGROUND: At least 13-20% of all Tuberculosis (TB) cases are recurrent TB. Recurrent TB has critical public health importance because recurrent TB patients have high risk of Multi-Drug Resistant TB (MDR-TB). It is critical to understand variations in the prevalence and treatment outcomes of recurrent TB between different geographical settings. The objective of our study was to estimate the prevalence of recurrent TB among TB cases and compare risk of unfavorable treatment outcomes between rural and urban settings. METHODS: In a retrospective cohort study conducted in southern province of Zambia, we used mixed effects logistic regression to asses associations between explanatory and outcome variables. Primary outcome was all-cause mortality and exposure was setting (rural/urban). Data was abstracted from the facility TB registers. RESULTS: Overall 3566 recurrent TB cases were diagnosed among 25,533 TB patients. The prevalence of recurrent TB was 15.3% (95% CI: 14.8 15.9) in urban and 11.3% (95% CI: 10.7 12.0) in rural areas. Death occurred in 197 (5.5%), 103 (2.9%) were lost to follow-up, and 113 (3.2%) failed treatment. Rural settings had 70% higher risk of death (adjusted OR: 1.7; 95% CI: 1.2 2.7). Risk of lost to follow-up was twice higher in rural than urban (adjusted OR: 2.0 95% CI: 1.3 3.0). Compared to HIV-uninfected, HIV-infected individuals on Antiretroviral Treatment (ART) were 70% more likely to die (adjusted OR: 1.7; 95% CI: 1.2 3.1). CONCLUSION: Recurrent TB prevalence was generally high in both urban and rural settings. The risk of mortality and lost to follow-up was higher among rural patients. We recommend a well-organized Directly Observed Therapy strategy adapted to setting where heightened TB control activities are focused on areas with poor treatment outcomes.

Proliferative and Invasive Colorectal Tumors in Pet Dogs Provide Unique Insights into Human Colorectal Cancer.

Spontaneous tumors in pet dogs represent a valuable but undercharacterized cancer model. To better use this resource, we performed an initial global comparison between proliferative and invasive colorectal tumors from 20 canine cases, and evaluated their molecular homology to human colorectal cancer (CRC). First, proliferative canine tumors harbor overactivated WNT/ß-catenin pathways and recurrent CTNNB1 (ß-catenin) mutations S45F/P, D32Y and G34E. Invasive canine tumors harbor prominent fibroblast proliferation and overactivated stroma. Both groups have recurrent TP53 mutations. We observed three invasion patterns in canine tumors: collective, crypt-like and epithelial⁻mesenchymal transition (EMT). We detected enriched Helicobacter bilis and Alistipes finegoldii in proliferative and crypt-like tumors, but depleted mucosa-microbes in the EMT tumor. Second, guided by our canine findings, we classified 79% of 478 human colon cancers from The Cancer Genome Atlas into four subtypes: primarily proliferative, or with collective, crypt-like or EMT invasion features. Their molecular characteristics match those of canine tumors. We showed that consensus molecular subtype 4 (mesenchymal) of human CRC should be further divided into EMT and crypt-like subtypes, which differ in TGF-ß activation and mucosa-microbe content. Our canine tumors share the same pathogenic pathway as human CRCs. Dog-human integration identifies three CRC invasion patterns and improves CRC subtyping.

SEG - A Software Program for Finding Somatic Copy Number Alterations in Whole Genome Sequencing Data of Cancer.

As next-generation sequencing technology advances and the cost decreases, whole genome sequencing (WGS) has become the preferred platform for the identification of somatic copy number alteration (CNA) events in cancer genomes. To more effectively decipher these massive sequencing data, we developed a software program named SEG, shortened from the word "segment". SEG utilizes mapped read or fragment density for CNA discovery. To reduce CNA artifacts arisen from sequencing and mapping biases, SEG first normalizes the data by taking the log2-ratio of each tumor density against its matching normal density. SEG then uses dynamic programming to find change-points among a contiguous log2-ratio data series along a chromosome, dividing the chromosome into different segments. SEG finally identifies those segments having CNA. Our analyses with both simulated and real sequencing data indicate that SEG finds more small CNAs than other published software tools.

Autotaxin exacerbates tumor progression by enhancing MEK1 and overriding the function of miR-489-3p.

Upregulated expression of autotaxin, a secreted phospholipase and phosphodiesterase enzyme, appears in malignant disease. The identification of a circulating miRNA signature should distinguish autotaxin-mediated disease and also elucidate unknown molecular mechanisms that rationalize its malignant potential. Using female transgenic 'AT-ATX' mice, whereby human wild-type autotaxin is expressed in liver under the control of the alpha-1 antitrypsin promoter, transgenic animals express augmented autotaxin in circulation and a percentage develop tumors. Serum collected at necropsy had circulating miRNAs analyzed for statistical significance. The ensuing autotaxin-mediated miRNome differentiated between groups: healthy FVB/N mice versus AT-ATX mice with and without tumors. Intriguingly, miR-489-3p was sharply increased in AT-ATX tumor-bearing mice. Tissue analysis showed a correlation between miR-489-3p expression in tumors and surrounding milieu with autotaxin concentration in circulation. Sequence alignment suggested miR-489-3p targets MEK1, which was confirmed through in vitro studies. Exogenously added miR-489-3p, which decreases MEK1 in normal cells, dramatically increased MEK1 expression in cells stably expressing autotaxin. Taken together, this suggests that autotaxin overrides the normal regulatory function of miR-489-3p to inhibit MEK1 via coordinately increased miR-489-3p appearing in serum.

The need for a network to establish and validate predictive biomarkers in cancer immunotherapy.

Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, the entire medical oncology field has been revolutionized by the introduction of immune checkpoints inhibitors. Despite success in a variety of malignancies, responses typically only occur in a small percentage of patients for any given histology or treatment regimen. There are also concerns that immunotherapies are associated with immune-related toxicity as well as high costs. As such, identifying biomarkers to determine which patients are likely to derive clinical benefit from which immunotherapy and/or be susceptible to adverse side effects is a compelling clinical and social need. In addition, with several new immunotherapy agents in different phases of development, and approved therapeutics being tested in combination with a variety of different standard of care treatments, there is a requirement to stratify patients and select the most appropriate population in which to assess clinical efficacy. The opportunity to design parallel biomarkers studies that are integrated within key randomized clinical trials could be the ideal solution. Sample collection (fresh and/or archival tissue, PBMC, serum, plasma, stool, etc.) at specific points of treatment is important for evaluating possible biomarkers and studying the mechanisms of responsiveness, resistance, toxicity and relapse. This white paper proposes the creation of a network to facilitate the sharing and coordinating of samples from clinical trials to enable more in-depth analyses of correlative biomarkers than is currently possible and to assess the feasibilities, logistics, and collated interests. We propose a high standard of sample collection and storage as well as exchange of samples and knowledge through collaboration, and envisage how this could move forward using banked samples from completed studies together with prospective planning for ongoing and future clinical trials.