Cross-validation approaches for penalized Cox regression.

Cross-validation is the most common way of selecting tuning parameters in penalized regression, but its use in penalized Cox regression models has received relatively little attention in the literature. Due to its partial likelihood construction, carrying out cross-validation for Cox models is not straightforward, and there are several potential approaches for implementation. Here, we propose a new approach based on cross-validating the linear predictors of the Cox model and compare it to approaches that have been proposed elsewhere. We show that the proposed approach offers an attractive balance of performance and numerical stability, and illustrate these advantages using simulated data as well as analyzing a high-dimensional study of gene expression and survival in lung cancer patients.

Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum.

BACKGROUND: Oculoauriculovertebral Spectrum (OAVS) encompasses abnormalities on derivatives from the first and second pharyngeal arches including macrostomia, hemifacial microsomia, micrognathia, preauricular tags, ocular and vertebral anomalies. We present genetic findings on a three-generation family affected with macrostomia, preauricular tags and uni- or bilateral ptosis following an autosomal dominant pattern. METHODS: We generated whole genome sequencing data for the proband, affected parent and unaffected paternal grandparent followed by Sanger sequencing on 23 family members for the top 10 candidate genes: KCND2, PDGFRA, CASP9, NCOA3, WNT10A, SIX1, MTF1, KDR/VEGFR2, LRRK1, and TRIM2 We performed parent and sibling-based transmission disequilibrium tests and burden analysis via a penalized linear mixed model, for segregation and mutation burden respectively. Next, via bioinformatic tools we predicted protein function, mutation pathogenicity and pathway enrichment to investigate the biological relevance of mutations identified. RESULTS: Rare missense mutations in SIX1, KDR/VEGFR2, and PDGFRA showed the best segregation with the OAV phenotypes in this family. When considering any of the 3 OAVS phenotypes as an outcome, SIX1 had the strongest associations in parent-TDTs and sib-TDTs (p=0.025, p=0.052) (unadjusted p-values). Burden analysis identified SIX1 (RC=0.87) and PDGFRA (RC=0.98) strongly associated with OAVS severity. Using phenotype-specific outcomes, sib-TDTs identified SIX1 with uni- or bilateral ptosis (p=0.049) and ear tags (p=0.01), and PDGFRA and KDR/VEGFR2 with ear tags (both p<0.01). CONCLUSION: SIX1, PDGFRA, and KDR/VEGFR2 are strongly associated to OAVS phenotypes. SIX1 has been previously associated with OAVS ear malformations and is co-expressed with EYA1 during ear development. Efforts to strengthen the genotype-phenotype co-relation underlying the OAVS are key to discover etiology, family counseling and prevention.

Intranasal Oxytocin Increases Head Motion During Functional MRI Scanning.

Oxytocin is a neuropeptide associated with prosocial behaviors, such as parent-child bonding, eye contact, and sexual activity. Intranasally-administered oxytocin has been widely used to study its effects on the brain using functional magnetic resonance imaging. Head motion is a significant confounding variable which was assessed as part of a double blind, placebo-controlled crossover study. Twenty-four mothers with drug addiction problems were initially recruited, along with 22 healthy control mothers, to test whether intranasal oxytocin enhances functional brain responses to images of their own versus unknown infant faces. Significant differences in head motion between oxytocin/placebo conditions and addiction/control groups were discovered. Administration of intranasal oxytocin was associated with more frequent counts of head motion exceeding 3 mm of framewise displacement, independent of group status (z=2.89, p=0.004). This effect was seen more strongly in the control group (z=2.30, p=0.02) than the addiction group (z=1.77, p=0.08). The addiction group was more likely to show increased head motion, independent of oxytocin or placebo condition (z=2.21, p=0.03). When examining the mean head motion across all time points, as opposed to the count of large movements, oxytocin's effect was limited to the addiction group (z=2.58, p=0.01), with a significant group by condition interaction effect observed. Intranasally-administered oxytocin may therefore have a confounding effect on functional MRI scanning results via its independent effect on head motion. These findings should be examined and replicated in other clinical populations.

Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets.

Progesterone prevents development of endometrial cancers through its receptor (PR) although the molecular mechanisms have yet to be fully characterized. In this study, we performed a global analysis of gene regulation by progesterone using human endometrial cancer cells that expressed PR endogenously or exogenously. We found progesterone strongly inhibits multiple components of the platelet derived growth factor receptor (PDGFR), Janus kinase (JAK), signal transducer and activator of transcription (STAT) pathway through PR. The PDGFR/JAK/STAT pathway signals to control numerous downstream targets including AP-1 transcription factors Fos and Jun. Treatment with inhibitors of the PDGFR/JAK/STAT pathway significantly blocked proliferation in multiple novel patient-derived organoid models of endometrial cancer, and activation of this pathway was found to be a poor prognostic signal for the survival of patients with endometrial cancer from The Cancer Genome Atlas. Our study identifies this pathway as central to the growth-limiting effects of progesterone in endometrial cancer and suggests that inhibitors of PDGFR/JAK/STAT should be considered for future therapeutic interventions.

CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression.

PURPOSE: Malignant peripheral nerve sheath tumors (MPNST) are lethal, Ras-driven sarcomas that lack effective therapies. We investigated effects of targeting cyclin-dependent kinases 4 and 6 (CDK4/6), MEK, and/or programmed death-ligand 1 (PD-L1) in preclinical MPNST models. EXPERIMENTAL DESIGN: Patient-matched MPNSTs and precursor lesions were examined by FISH, RNA sequencing, IHC, and Connectivity-Map analyses. Antitumor activity of CDK4/6 and MEK inhibitors was measured in MPNST cell lines, patient-derived xenografts (PDX), and de novo mouse MPNSTs, with the latter used to determine anti-PD-L1 response. RESULTS: Patient tumor analyses identified CDK4/6 and MEK as actionable targets for MPNST therapy. Low-dose combinations of CDK4/6 and MEK inhibitors synergistically reactivated the retinoblastoma (RB1) tumor suppressor, induced cell death, and decreased clonogenic survival of MPNST cells. In immune-deficient mice, dual CDK4/6-MEK inhibition slowed tumor growth in 4 of 5 MPNST PDXs. In immunocompetent mice, combination therapy of de novo MPNSTs caused tumor regression, delayed resistant tumor outgrowth, and improved survival relative to monotherapies. Drug-sensitive tumors that regressed contained plasma cells and increased cytotoxic T cells, whereas drug-resistant tumors adopted an immunosuppressive microenvironment with elevated MHC II-low macrophages and increased tumor cell PD-L1 expression. Excitingly, CDK4/6-MEK inhibition sensitized MPNSTs to anti-PD-L1 immune checkpoint blockade (ICB) with some mice showing complete tumor regression. CONCLUSIONS: CDK4/6-MEK inhibition induces a novel plasma cell-associated immune response and extended antitumor activity in MPNSTs, which dramatically enhances anti-PD-L1 therapy. These preclinical findings provide strong rationale for clinical translation of CDK4/6-MEK-ICB targeted therapies in MPNST as they may yield sustained antitumor responses and improved patient outcomes.

Feature-specific inference for penalized regression using local false discovery rates.

Penalized regression methods such as the lasso are a popular approach to analyzing high-dimensional data. One attractive property of the lasso is that it naturally performs variable selection. An important area of concern, however, is the reliability of these selections. Motivated by local false discovery rate methodology from the large-scale hypothesis testing literature, we propose a method for calculating a local false discovery rate for each variable under consideration by the lasso model. These rates can be used to assess the reliability of an individual feature, or to estimate the model's overall false discovery rate. The method can be used for any level of regularization. This is particularly useful for models with a few highly significant features but a high overall false discovery rate, a relatively common occurrence when using cross validation to select a model. It is also flexible enough to be applied to many varieties of penalized likelihoods including generalized linear models and Cox regression, and a variety of penalties, including the minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) penalty. We demonstrate the validity of this approach and contrast it with other inferential methods for penalized regression as well as with local false discovery rates for univariate hypothesis tests. Finally, we show the practical utility of our method by applying it to a case study involving gene expression in breast cancer patients.

Surgical Management of G3 Gastroenteropancreatic Neuroendocrine Neoplasms: A Systematic Review and Meta-analysis.

BACKGROUND: Grade 3 (G3) gastroenteropancreatic (GEP) neuroendocrine neoplasms (NENs) are rare, aggressive tumors with poor prognosis. The World Health Organization 2017 and 2019 classifications further subdivided G3 NENs into G3 neuroendocrine tumors (NETs) and neuroendocrine carcinomas (NECs). Current guidelines favor medical management in most of these patients, and the role of surgical management is not well defined. We performed a systematic literature review and meta-analysis of surgical management versus nonsurgical management for G3 GEP NENs. MATERIALS AND METHODS: A PRISMA-compliant systematic review of the MEDLINE, Embase, Scopus, and Cochrane Library databases (end-of-search date: 16 July 2021) was conducted. Individual patient survival data were reconstructed, and random-effects meta-analyses were performed. RESULTS: Fourteen studies comprising 1810 surgical and 910 nonsurgical patients were systematically reviewed. Publication bias adjusted meta-analysis of 12 studies (1788 surgical and 857 nonsurgical patients) showed increased overall survival (OS) after surgical compared with nonsurgical management for G3 GEP NENs [hazard ratio (HR) 0.40, 95% confidence interval (CI) 0.31-0.53]. Subgroup meta-analyses showed increased OS after surgical management for both pancreatic and gastrointestinal primary sites separately. In another subgroup meta-analysis of G3 GEP NETs (not NECs), surgical management was associated with increased OS compared with nonsurgical management (HR 0.26, 95% CI 0.11-0.61). CONCLUSIONS: Surgical management of G3 GEP NENs may provide a potential survival benefit in well-selected cases. Further research is needed to define which patients will benefit most from surgical versus nonsurgical management. The current literature is limited by inconsistent reporting of survival outcomes in surgical versus nonsurgical groups, tumor grade, differentiation, primary tumor site, and selection criteria for surgical and nonsurgical management.

Hypertensive disorders of pregnancy among women with a history of leukemia or lymphoma.

OBJECTIVE: Hypertension during pregnancy can adversely affect maternal and fetal health. This study assessed whether diagnosis of leukemia or lymphoma prior to pregnancy is associated with hypertensive disorders of pregnancy including gestational hypertension, preeclampsia and eclampsia. STUDY DESIGN: A cross-sectional study used two statewide population-based datasets that linked birth certificates with sources of maternal medical history: hospital discharges in California and Surveillance, Epidemiology, and End Results (SEER) cancer registry data in Iowa. Birth years included 2007-2012 in California and 1989-2018 in Iowa. MAIN OUTCOME MEASURES: Primary outcome measure was hypertension in pregnancy measured from combined birth certificate and hospital diagnoses in California (for gestational hypertension, preeclampsia, or eclampsia) and birth certificate information (gestational hypertension or eclampsia) in Iowa. RESULTS: After adjusting for maternal age, race, education, smoking, and plurality, those with a history of leukemia/lymphoma were at increased risk of hypertensive disorders of pregnancy in Iowa (odds ratio (OR) = 1.86; 95% CI 1.07-3.23), but not in California (OR = 1.12; 95% CI 0.87-1.43). In sensitivity analysis restricting to more severe forms of hypertension in pregnancy (preeclampsia and eclampsia) in the California cohort, the effect estimate increased (OR = 1.29; 95% CI 0.96-1.74). CONCLUSION: In a population-based linked cancer registry-birth certificate study, an increased risk of hypertensive disorders of pregnancy was observed among leukemia or lymphoma survivors. Findings were consistent but non-significant in a second, more ethnically diverse study population with less precise cancer history data. Improved monitoring and surveillance may be warranted for leukemia or lymphoma survivors throughout their pregnancies.

Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo.

Background: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas with complex molecular and genetic alterations. Powerful tumor suppressors CDKN2A and TP53 are commonly disrupted along with NF1, a gene that encodes a negative regulator of Ras. Many additional factors have been implicated in MPNST pathogenesis. A greater understanding of critical drivers of MPNSTs is needed to guide more informed targeted therapies for patients. RABL6A is a newly identified driver of MPNST cell survival and proliferation whose in vivo role in the disease is unknown. Methods: Using CRISPR-Cas9 targeting of Nf1 + Cdkn2a or Nf1 + Tp53 in the mouse sciatic nerve to form de novo MPNSTs, we investigated the biological significance of RABL6A in MPNST development. Terminal tumors were evaluated by western blot, qRT-PCR, and immunohistochemistry. Results: Mice lacking Rabl6 displayed slower tumor progression and extended survival relative to wildtype animals in both genetic contexts. YAP oncogenic activity was selectively downregulated in Rabl6-null, Nf1 + Cdkn2a lesions whereas loss of RABL6A caused upregulation of the CDK inhibitor, p27, in all tumors. Paradoxically, both models displayed elevated Myc protein and Ki67 staining in terminal tumors lacking RABL6A. In Nf1 + p53 tumors, cellular atypia and polyploidy were evident and increased by RABL6A loss. Conclusions: These findings demonstrate that RABL6A is required for optimal progression of NF1 mutant MPNSTs in vivo in both Cdkn2a and p53 inactivated settings. However, sustained RABL6A loss may provide selective pressure for unwanted alterations, including increased Myc, cellular atypia, and polyploidy, that ultimately promote a hyper-proliferative tumor phenotype akin to drug-resistant lesions.

The risk of preterm birth among women with a history of leukemia or lymphoma.

OBJECTIVE: Leukemia and lymphoma are top cancers affecting children, adolescents and young adults with high five-year survival rates. Late effects of these cancers are a concern in reproductive-age patients, including pregnancy outcomes such as preterm birth. Our study aimed to evaluate whether diagnosis of leukemia or lymphoma prior to pregnancy was associated with preterm birth (<37 weeks gestation). METHODS: We conducted a cross-sectional study using a population-based dataset from California with linked birth certificates to hospital discharge records and an Iowa-based sample that linked birth certificates to Surveillance, Epidemiology, and End Results (SEER) cancer registry data. Preterm birth was defined using birth certificates. We ascertained history of leukemia and lymphoma using discharge diagnosis data in California and SEER registry in Iowa. RESULTS: Prevalence of preterm birth in California and Iowa was 14.6% and 12.0%, respectively, in women with a history of leukemia/lymphoma compared to 7.8% and 8.2%, respectively, in women without a cancer history. After adjusting for maternal age, race, education, smoking, and plurality, Women with history of leukemia/lymphoma were at an increased risk of having a preterm birth in California (odds ratio (OR) 1.89; 95% confidence interval (CI) 1.56-2.28) and Iowa (OR 1.61; 95% CI 1.10-2.37) compared to those with no cancer history. CONCLUSION: In both California and Iowa, women with a history of leukemia or lymphoma were at increased risk for preterm birth. This suggests the importance of counseling with a history of leukemia/lymphoma prior to pregnancy and increased monitoring of women during pregnancy.

Metabolic differences among newborns born to mothers with a history of leukemia or lymphoma.

BACKGROUND: Leukemia and lymphoma are cancers affecting children, adolescents, and young adults and may affect reproductive outcomes and maternal metabolism. We evaluated for metabolic changes in newborns of mothers with a history of these cancers. METHODS: A cross-sectional study was conducted on California births from 2007 to 2011 with linked maternal hospital discharge records, birth certificate, and newborn screening metabolites. History of leukemia or lymphoma was determined using ICD-9-CM codes from hospital discharge data and newborn metabolite data from the newborn screening program. RESULTS: A total of 2,068,038 women without cancer history and 906 with history of leukemia or lymphoma were included. After adjusting for differences in maternal age, infant sex, age at metabolite collection, gestational age, and birthweight, among newborns born to women with history of leukemia/lymphoma, several acylcarnitines were significantly (p < .001 - based on Bonferroni correction for multiple testing) higher compared to newborns of mothers without cancer history: C3-DC (mean difference (MD) = 0.006), C5-DC (MD = 0.009), C8:1 (MD = 0.008), C14 (MD = 0.010), and C16:1 (MD = 0.011), whereas citrulline levels were significantly lower (MD = -0.581) among newborns born to mothers with history of leukemia or lymphoma compared to newborns of mothers without a history of cancer. CONCLUSION: The varied metabolite levels suggest history of leukemia or lymphoma has metabolic impact on newborn offspring, which may have implications for future metabolic consequences such as necrotizing enterocolitis and urea cycle enzyme disorders in children born to mothers with a history of leukemia or lymphoma.

RABL6A Promotes Pancreatic Neuroendocrine Tumor Angiogenesis and Progression In Vivo.

Pancreatic neuroendocrine tumors (pNETs) are difficult-to-treat neoplasms whose incidence is rising. Greater understanding of pNET pathogenesis is needed to identify new biomarkers and targets for improved therapy. RABL6A, a novel oncogenic GTPase, is highly expressed in patient pNETs and required for pNET cell proliferation and survival in vitro. Here, we investigated the role of RABL6A in pNET progression in vivo using a well-established model of the disease. RIP-Tag2 (RT2) mice develop functional pNETs (insulinomas) due to SV40 large T-antigen expression in pancreatic islet ß cells. RABL6A loss in RT2 mice significantly delayed pancreatic tumor formation, reduced tumor angiogenesis and mitoses, and extended survival. Those effects correlated with upregulation of anti-angiogenic p19ARF and downregulation of proangiogenic c-Myc in RABL6A-deficient islets and tumors. Our findings demonstrate that RABL6A is a bona fide oncogenic driver of pNET angiogenesis and development in vivo.

Development and comparison of novel bioluminescent mouse models of pancreatic neuroendocrine neoplasm metastasis.

Pancreatic neuroendocrine neoplasms (pNENs) are slow growing cancers of increasing incidence that lack effective treatments once they become metastatic. Unfortunately, nearly half of pNEN patients present with metastatic liver tumors at diagnosis and current therapies fail to improve overall survival. Pre-clinical models of pNEN metastasis are needed to advance our understanding of the mechanisms driving the metastatic process and for the development of novel, targeted therapeutic interventions. To model metastatic dissemination of tumor cells, human pNEN cell lines (BON1 and Qgp1) stably expressing firefly luciferase (luc) were generated and introduced into NSG immunodeficient mice by intracardiac (IC) or intravenous (IV) injection. The efficiency, kinetics and distribution of tumor growth was evaluated weekly by non-invasive bioluminescent imaging (BLI). Tumors formed in all animals in both the IC and IV models. Bioluminescent Qgp1.luc cells preferentially metastasized to the liver regardless of delivery route, mimicking the predominant site of pNEN metastasis in patients. By comparison, BON1.luc cells most commonly formed lung tumors following either IV or IC administration and colonized a wider variety of tissues than Qgp1.luc cells. These models provide a unique platform for testing candidate metastasis genes and anti-metastatic therapies for pNENs.

Penalized linear mixed models for structured genetic data.

Many genetic studies that aim to identify genetic variants associated with complex phenotypes are subject to unobserved confounding factors arising from environmental heterogeneity. This poses a challenge to detecting associations of interest and is known to induce spurious associations when left unaccounted for. Penalized linear mixed models (LMMs) are an attractive method to correct for unobserved confounding. These methods correct for varying levels of relatedness and population structure by modeling it as a random effect with a covariance structure estimated from observed genetic data. Despite an extensive literature on penalized regression and LMMs separately, the two are rarely discussed together. The aim of this review is to do so while examining the statistical properties of penalized LMMs in the genetic association setting. Specifically, the ability of penalized LMMs to accurately estimate genetic effects in the presence of environmental confounding has not been well studied. To clarify the important yet subtle distinction between population structure and environmental heterogeneity, we present a detailed review of relevant concepts and methods. In addition, we evaluate the performance of penalized LMMs and competing methods in terms of estimation and selection accuracy in the presence of a number of confounding structures.

Prognostic and therapeutic value of the Hippo pathway, RABL6A, and p53-MDM2 axes in sarcomas.

Additional prognostic and therapeutic biomarkers effective across different histological types of sarcoma are needed. Herein we evaluate expression of TAZ and YAP, the p53-MDM2 axis, and RABL6A, a novel oncoprotein with potential ties to both pathways, in sarcomas of different histological types. Immunohistochemical staining of a tissue microarray including 163 sarcomas and correlation with clinical data showed that elevated YAP and TAZ independently predict worse overall and progression-free survival, respectively. In the absence of p53 expression, combined TAZ and YAP expression adversely affect overall, progression free, and metastasis free survival more than TAZ or YAP activation alone. RABL6A independently predicted shorter time to metastasis and was positively correlated with p53, MDM2 and YAP expression, supporting a possible functional relationship between the biomarkers. Network analysis further showed that TAZ is positively correlated with MDM2 expression. The data implicate all five proteins as clinically relevant downstream players in the Hippo pathway. Finally, a novel inhibitor of MDM2 (MA242), effectively suppressed the survival of sarcoma cell lines from different histological types regardless of p53 status. These findings suggest both independent and cooperative roles for all five biomarkers across different histological types of sarcoma in predicting patient outcomes and potentially guiding future therapeutic approaches.

Presacral neuroendocrine tumors associated with the Currarino syndrome.

Currarino syndrome (CS) is an autosomal dominant syndrome caused by mutations in MNX1 and characterized by anorectal abnormalities, partial sacral agenesis, and presacral masses. The presacral masses are typically benign; however, malignant degeneration can occur, and presacral neuroendocrine tumors (NETs) have been reported in six cases. We report three individuals from two families affected by CS in which multiple individuals developed presacral NETs. The first family, 491, had six members with features of CS, including two siblings who presented with presacral, Grade 2 NETs, one of which had metastasized to bone and lymph nodes. A germline c.874C>T (p.Arg292Trp) mutation was found in a highly conserved region of MNX1 in three affected members who underwent sequencing. A second somatic variant/deletion in MNX1 was not detected in either patient's tumor. In the second family, 342, the proband presented with an incidentally discovered presacral NET. The proband's father had previously undergone resection of a presacral NET, and so genetic testing was performed, which did not reveal an MNX1 mutation or copy number variants. The lack of a second, somatic mutation in the tumors from family 491 argues against MNX1 acting as a tumor suppressor, and the absence of a germline MNX1 mutation in family 342 suggests that other genetic and anatomic factors contribute to the development of presacral NETs. These cases highlight the variable presentation of CS, and the potential for malignancy in these patients.

Perinatal determinants of growth trajectories in children born preterm.

BACKGROUND: A growing amount of evidence indicates in utero and early life growth has profound, long-term consequences for an individual's health throughout the life course; however, there is limited data in preterm infants, a vulnerable population at risk for growth abnormalities. OBJECTIVE: To address the gap in knowledge concerning early growth and its determinants in preterm infants. METHODS: A retrospective cohort study was performed using a population of preterm (< 37 weeks gestation) infants obtained from an electronic medical record database. Weight z-scores were acquired from discharge until roughly two years corrected age. Linear mixed effects modeling, with random slopes and intercepts, was employed to estimate growth trajectories. RESULTS: Thirteen variables, including maternal race, hypertension during pregnancy, preeclampsia, first trimester body mass index, multiple status, gestational age, birth weight, birth length, head circumference, year of birth, length of birth hospitalization stay, total parenteral nutrition, and dextrose treatment, were significantly associated with growth rates of preterm infants in univariate analyses. A small percentage (1.32% - 2.07%) of the variation in the growth of preterm infants can be explained in a joint model of these perinatal factors. In extremely preterm infants, additional variation in growth trajectories can be explained by conditions whose risk differs by degree of prematurity. Specifically, infants with periventricular leukomalacia or retinopathy of prematurity experienced decelerated rates of growth compared to infants without such conditions. CONCLUSIONS: Factors found to influence growth over time in children born at term also affect growth of preterm infants. The strength of association and the magnitude of the effect varied by gestational age, revealing that significant heterogeneity in growth and its determinants exists within the preterm population.

Locally invasive, castrate-resistant prostate cancer in a Pten/Trp53 double knockout mouse model of prostate cancer monitored with non-invasive bioluminescent imaging.

Here we have improved an existing mouse model of prostate cancer based on prostate-specific deletion of Pten and Trp53 by incorporating a Cre-activatable luciferase reporter. By coupling the deletion of those genes to the activation of a luciferase reporter, we were able to monitor tumor burden non-invasively over time. We show that, consistent with previous reports, deletion of both Pten and Trp53 on a C57BL/6 background accelerates tumor growth and results in both the loss of androgen receptor expression and castrate resistant tumors as compared with loss of Pten alone. Loss of Trp53 results in the development of sarcomatoid histology and the expression of markers of epithelial-to-mesenchymal transition Zeb1 and vimentin, with kinetics and penetrance dependent on whether one or both alleles of Trp53 were deleted. Homozygous deletion of Trp53 and Pten resulted in uniformly lethal disease by 25 weeks. While we were able to detect locally invasive disease in the peritoneal cavity in aggressive tumors from the double knockout mice, we were unable to detect lymphatic or hematogenous metastatic disease in lymph nodes or at distant sites.

Encoding the Odor of Cigarette Smoke.

The encoding of odors is believed to begin as a combinatorial code consisting of distinct patterns of responses from odorant receptors (ORs), trace-amine associated receptors (TAARs), or both. To determine how specific response patterns arise requires detecting patterns in vivo and understanding how the components of an odor, which are nearly always mixtures of odorants, give rise to parts of the pattern. Cigarette smoke, a common and clinically relevant odor consisting of >400 odorants, evokes responses from 144 ORs and 3 TAARs in freely behaving male and female mice, the first example of in vivo responses of both ORs and TAARs to an odor. As expected, a simplified artificial mimic of cigarette smoke odor tested at low concentration to identify highly sensitive receptors evokes responses from four ORs, all also responsive to cigarette smoke. Human subjects of either sex identify 1-pentanethiol as the odorant most critical for perception of the artificial mimic; and in mice the OR response patterns to these two odors are significantly similar. Fifty-eight ORs respond to the headspace above 25% 1-pentanethiol, including 9 ORs responsive to cigarette smoke. The response patterns to both cigarette smoke and 1-pentanethiol have strongly responsive ORs spread widely across OR sequence diversity, consistent with most other combinatorial codes previously measured in vivo The encoding of cigarette smoke is accomplished by a broad receptor response pattern, and 1-pentanethiol is responsible for a small subset of the responsive ORs in this combinatorial code.SIGNIFICANCE STATEMENT Complex odors are usually perceived as distinct odor objects. Cigarette smoke is the first complex odor whose in vivo receptor response pattern has been measured. It is also the first pattern shown to include responses from both odorant receptors and trace-amine associated receptors, confirming that the encoding of complex odors can be enriched by signals coming through both families of receptors. Measures of human perception and mouse receptor physiology agree that 1-pentanethiol is a critical component of a simplified odorant mixture designed to mimic cigarette smoke odor. Its receptor response pattern helps to link those of the artificial mimic and real cigarette smoke, consistent with expectations about perceptual similarity arising from shared elements in receptor response patterns.