Tumor Evolution and Drug Response in Patient-Derived Organoid Models of Bladder Cancer.

Bladder cancer is the fifth most prevalent cancer in the U.S., yet is understudied, and few laboratory models exist that reflect the biology of the human disease. Here, we describe a biobank of patient-derived organoid lines that recapitulates the histopathological and molecular diversity of human bladder cancer. Organoid lines can be established efficiently from patient biopsies acquired before and after disease recurrence and are interconvertible with orthotopic xenografts. Notably, organoid lines often retain parental tumor heterogeneity and exhibit a spectrum of genomic changes that are consistent with tumor evolution in culture. Analyses of drug response using bladder tumor organoids show partial correlations with mutational profiles, as well as changes associated with treatment resistance, and specific responses can be validated using xenografts in vivo. Our studies indicate that patient-derived bladder tumor organoids represent a faithful model system for studying tumor evolution and treatment response in the context of precision cancer medicine.

Implementing Genome-Driven Oncology.

Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment.

KRAS Allelic Imbalance Enhances Fitness and Modulates MAP Kinase Dependence in Cancer.

Investigating therapeutic "outliers" that show exceptional responses to anti-cancer treatment can uncover biomarkers of drug sensitivity. We performed preclinical trials investigating primary murine acute myeloid leukemias (AMLs) generated by retroviral insertional mutagenesis in KrasG12D "knockin" mice with the MEK inhibitor PD0325901 (PD901). One outlier AML responded and exhibited intrinsic drug resistance at relapse. Loss of wild-type (WT) Kras enhanced the fitness of the dominant clone and rendered it sensitive to MEK inhibition. Similarly, human colorectal cancer cell lines with increased KRAS mutant allele frequency were more sensitive to MAP kinase inhibition, and CRISPR-Cas9-mediated replacement of WT KRAS with a mutant allele sensitized heterozygous mutant HCT116 cells to treatment. In a prospectively characterized cohort of patients with advanced cancer, 642 of 1,168 (55%) with KRAS mutations exhibited allelic imbalance. These studies demonstrate that serial genetic changes at the Kras/KRAS locus are frequent in cancer and modulate competitive fitness and MEK dependency.

ARAF protein kinase activates RAS by antagonizing its binding to RASGAP NF1.

RAF protein kinases are effectors of the GTP-bound form of small guanosine triphosphatase RAS and function by phosphorylating MEK. We showed here that the expression of ARAF activated RAS in a kinase-independent manner. Binding of ARAF to RAS displaced the GTPase-activating protein NF1 and antagonized NF1-mediated inhibition of RAS. This reduced ERK-dependent inhibition of RAS and increased RAS-GTP. By this mechanism, ARAF regulated the duration and consequences of RTK-induced RAS activation and supported the RAS output of RTK-dependent tumor cells. In human lung cancers with EGFR mutation, amplification of ARAF was associated with acquired resistance to EGFR inhibitors, which was overcome by combining EGFR inhibitors with an inhibitor of the protein tyrosine phosphatase SHP2 to enhance inhibition of nucleotide exchange and RAS activation.

Anatomic position determines oncogenic specificity in melanoma.

Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programmes in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma and enrichment for CRKL amplifications in acral melanoma. We modelled these changes in transgenic zebrafish models and found that CRKL-driven tumours formed predominantly in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin and limb melanocytes, when compared with body melanocytes, revealed a positional identity gene programme typified by posterior HOX13 genes. This positional gene programme synergized with CRKL to amplify insulin-like growth factor (IGF) signalling and drive tumours at acral sites. Abrogation of this CRKL-driven programme eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

Phase and context shape the function of composite oncogenic mutations.

Cancers develop as a result of driver mutations1,2 that lead to clonal outgrowth and the evolution of disease3,4. The discovery and functional characterization of individual driver mutations are central aims of cancer research, and have elucidated myriad phenotypes5 and therapeutic vulnerabilities6. However, the serial genetic evolution of mutant cancer genes7,8 and the allelic context in which they arise is poorly understood in both common and rare cancer genes and tumour types. Here we find that nearly one in four human tumours contains a composite mutation of a cancer-associated gene, defined as two or more nonsynonymous somatic mutations in the same gene and tumour. Composite mutations are enriched in specific genes, have an elevated rate of use of less-common hotspot mutations acquired in a chronology driven in part by oncogenic fitness, and arise in an allelic configuration that reflects context-specific selective pressures. cis-acting composite mutations are hypermorphic in some genes in which dosage effects predominate (such as TERT), whereas they lead to selection of function in other genes (such as TP53). Collectively, composite mutations are driver alterations that arise from context- and allele-specific selective pressures that are dependent in part on gene and mutation function, and which lead to complex-often neomorphic-functions of biological and therapeutic importance.

Author Correction: Tumour lineage shapes BRCA-mediated phenotypes.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Tumour lineage shapes BRCA-mediated phenotypes.

Mutations in BRCA1 and BRCA2 predispose individuals to certain cancers1-3, and disease-specific screening and preventative strategies have reduced cancer mortality in affected patients4,5. These classical tumour-suppressor genes have tumorigenic effects associated with somatic biallelic inactivation, although haploinsufficiency may also promote the formation and progression of tumours6,7. Moreover, BRCA1/2-mutant tumours are often deficient in the repair of double-stranded DNA breaks by homologous recombination8-13, and consequently exhibit increased therapeutic sensitivity to platinum-containing therapy and inhibitors of poly-(ADP-ribose)-polymerase (PARP)14,15. However, the phenotypic and therapeutic relevance of mutations in BRCA1 or BRCA2 remains poorly defined in most cancer types. Here we show that in the 2.7% and 1.8% of patients with advanced-stage cancer and germline pathogenic or somatic loss-of-function alterations in BRCA1/2, respectively, selective pressure for biallelic inactivation, zygosity-dependent phenotype penetrance, and sensitivity to PARP inhibition were observed only in tumour types associated with increased heritable cancer risk in BRCA1/2 carriers (BRCA-associated cancer types). Conversely, among patients with non-BRCA-associated cancer types, most carriers of these BRCA1/2 mutation types had evidence for tumour pathogenesis that was independent of mutant BRCA1/2. Overall, mutant BRCA is an indispensable founding event for some tumours, but in a considerable proportion of other cancers, it appears to be biologically neutral-a difference predominantly conditioned by tumour lineage-with implications for disease pathogenesis, screening, design of clinical trials and therapeutic decision-making.

Author Correction: HER kinase inhibition in patients with HER2- and HER3-mutant cancers.

The 'Competing interests' statement of this Article has been updated; please see the accompanying Amendment. The original Article has not been corrected online.

Associations between type 1 diabetes and educational outcomes: an Aotearoa/New Zealand nationwide birth cohort study using the Integrated Data Infrastructure.

AIMS/HYPOTHESIS: Type 1 diabetes is one of the most common chronic diseases of childhood. It is hypothesised that the metabolic and psychosocial consequences of type 1 diabetes may affect educational outcomes; however, existing literature presents conflicting results. This study aimed to assess whether educational outcomes differ for young people with and without type 1 diabetes in Aotearoa/New Zealand (NZ). METHODS: This was a nationwide 9 year birth cohort study of all people born in NZ from 1993 to 2001 using linked administrative data held within the Integrated Data Infrastructure, a national research database containing linked health and non-health data. Educational outcomes of high school attainment, high school attendance and university enrolment were measured from age 13 years until 20 years. Generalised linear regression models with log link and Gaussian distributions were used to compare educational outcomes between those with and those without type 1 diabetes, adjusting for sociodemographic and maternal characteristics. RESULTS: Of the 442,320 children in the birth cohort, type 1 diabetes was identified in 2058 (0.47%) (mean [SD] age of type 1 diabetes diagnosis 7.7 [3.4] years). Educational outcomes were significantly lower for children with type 1 diabetes than for those without type 1 diabetes, including for any high school qualification (RR 0.97 [95% CI 0.95, 0.99]), university entrance-level high school attainment (RR 0.88 [95% CI 0.84, 0.92]), regular high school attendance (RR 0.91 [95% CI 0.85, 0.97]) and university enrolment (RR 0.93 [95% CI 0.88, 0.98]), even after adjusting for sociodemographic and maternal factors. In addition, educational outcomes were substantially lower for those with post type 1 diabetes diagnosis hospitalisations for diabetic ketoacidosis and hypoglycaemia. CONCLUSIONS/INTERPRETATION: In this whole NZ birth cohort study, type 1 diabetes was associated with lower educational outcomes spanning secondary school and into university enrolment. Ongoing efforts to support students with type 1 diabetes are needed, particularly for those with a greater risk profile.

HER kinase inhibition in patients with HER2- and HER3-mutant cancers.

Somatic mutations of ERBB2 and ERBB3 (which encode HER2 and HER3, respectively) are found in a wide range of cancers. Preclinical modelling suggests that a subset of these mutations lead to constitutive HER2 activation, but most remain biologically uncharacterized. Here we define the biological and therapeutic importance of known oncogenic HER2 and HER3 mutations and variants of unknown biological importance by conducting a multi-histology, genomically selected, 'basket' trial using the pan-HER kinase inhibitor neratinib (SUMMIT; clinicaltrials.gov identifier NCT01953926). Efficacy in HER2-mutant cancers varied as a function of both tumour type and mutant allele to a degree not predicted by preclinical models, with the greatest activity seen in breast, cervical and biliary cancers and with tumours that contain kinase domain missense mutations. This study demonstrates how a molecularly driven clinical trial can be used to refine our biological understanding of both characterized and new genomic alterations with potential broad applicability for advancing the paradigm of genome-driven oncology.

Tumours with class 3 BRAF mutants are sensitive to the inhibition of activated RAS.

Approximately 200 BRAF mutant alleles have been identified in human tumours. Activating BRAF mutants cause feedback inhibition of GTP-bound RAS, are RAS-independent and signal either as active monomers (class 1) or constitutively active dimers (class 2). Here we characterize a third class of BRAF mutants-those that have impaired kinase activity or are kinase-dead. These mutants are sensitive to ERK-mediated feedback and their activation of signalling is RAS-dependent. The mutants bind more tightly than wild-type BRAF to RAS-GTP, and their binding to and activation of wild-type CRAF is enhanced, leading to increased ERK signalling. The model suggests that dysregulation of signalling by these mutants in tumours requires coexistent mechanisms for maintaining RAS activation despite ERK-dependent feedback. Consistent with this hypothesis, melanomas with these class 3 BRAF mutations also harbour RAS mutations or NF1 deletions. By contrast, in lung and colorectal cancers with class 3 BRAF mutants, RAS is typically activated by receptor tyrosine kinase signalling. These tumours are sensitive to the inhibition of RAS activation by inhibitors of receptor tyrosine kinases. We have thus defined three distinct functional classes of BRAF mutants in human tumours. The mutants activate ERK signalling by different mechanisms that dictate their sensitivity to therapeutic inhibitors of the pathway.

Identifying neurodevelopmental disabilities from nationalised preschool health check.

OBJECTIVE: Models of psychometric screening to identify individuals with neurodevelopmental disabilities (NDDs) have had limited success. In Aotearoa/New Zealand, routine developmental surveillance of preschool children is undertaken using the Before School Check (B4SC), which includes psychometric and physical health screening instruments. This study aimed to determine whether combining multiple screening measures could improve the prediction of NDDs. METHODS: Linked administrative health data were used to identify NDDs, including attention deficit hyperactivity disorder, autism spectrum disorder and intellectual disability, within a multi-year national cohort of children who undertook the B4SC. Cox proportional hazards models, with different combinations of potential predictors, were used to predict onset of a NDD. Harrell's c-statistic for composite models were compared with a model representing recommended cutoff psychometric scores for referral in New Zealand. RESULTS: Data were examined for 287,754 children, and NDDs were identified in 10,953 (3.8%). The best-performing composite model combining the Strengths and Difficulties Questionnaire, the Parental Evaluation of Developmental Status, vision screening and biological sex had 'excellent' predictive power (C-statistic: 0.83) compared with existing referral pathways which had 'poor' predictive power (C-statistic: 0.68). In addition, the composite model was able to improve the sensitivity of NDD diagnosis detection by 13% without any reduction in specificity. CONCLUSIONS: Combination of B4SC screening measures using composite modelling could lead to significantly improved identification of preschool children with NDDs when compared with surveillance that rely on individual psychometric test results alone. This may optimise access to academic, personal and family support for children with NDDs.

Regional variation in sudden unexpected death in infancy in New Zealand.

AIM: To estimate the relative risk of sudden unexpected death in infancy (SUDI) by district health board (DHB) in New Zealand after adjustment for socio-economic deprivation, ethnicity and other demographic factors. METHODS: We conducted a population-based cohort study using data from the Integrated Data Infrastructure, a large research database containing linked data from a range of government agencies. The study population was all live births and their mothers in New Zealand from 2012 to 2018. The exposure of interest was DHB. The outcome was SUDI. RESULTS: There were 418 068 live births in New Zealand from 2012 to 2018, and of these 415 401 (99.4%) had valid DHB data. There was considerable variation in the proportion of infants in each DHB living in the most deprived decile varying from 4.5% in Nelson, West Coast and Canterbury to 29.7% in Counties Manukau. There were 267 SUDI cases, giving an overall rate of 0.64/1000 live births during the study period (2012-2018). The SUDI rate varied from 1.11/1000 in Northland to 0.30/1000 in Waitemata and Auckland. Counties Manukau had the largest number of deaths (n = 54; rate = 1.08/1000). Five DHB regions had increased risk of SUDI compared to the reference group but, after adjustment, no DHB was significantly increased. CONCLUSIONS: This study found that there is marked variation in SUDI risk by DHB, but this is explained by socio-economic and demographic variation within DHBs. This study emphasises the importance of the contribution of social determinants of health to SUDI.

Modeling cancer genomic data in yeast reveals selection against ATM function during tumorigenesis.

The DNA damage response (DDR) comprises multiple functions that collectively preserve genomic integrity and suppress tumorigenesis. The Mre11 complex and ATM govern a major axis of the DDR and several lines of evidence implicate that axis in tumor suppression. Components of the Mre11 complex are mutated in approximately five percent of human cancers. Inherited mutations of complex members cause severe chromosome instability syndromes, such as Nijmegen Breakage Syndrome, which is associated with strong predisposition to malignancy. And in mice, Mre11 complex mutations are markedly more susceptible to oncogene- induced carcinogenesis. The complex is integral to all modes of DNA double strand break (DSB) repair and is required for the activation of ATM to effect DNA damage signaling. To understand which functions of the Mre11 complex are important for tumor suppression, we undertook mining of cancer genomic data from the clinical sequencing program at Memorial Sloan Kettering Cancer Center, which includes the Mre11 complex among the 468 genes assessed. Twenty five mutations in MRE11 and RAD50 were modeled in S. cerevisiae and in vitro. The mutations were chosen based on recurrence and conservation between human and yeast. We found that a significant fraction of tumor-borne RAD50 and MRE11 mutations exhibited separation of function phenotypes wherein Tel1/ATM activation was severely impaired while DNA repair functions were mildly or not affected. At the molecular level, the gene products of RAD50 mutations exhibited defects in ATP binding and hydrolysis. The data reflect the importance of Rad50 ATPase activity for Tel1/ATM activation and suggest that inactivation of ATM signaling confers an advantage to burgeoning tumor cells.

Further reductions in the prevalence of obesity in 4-year-old New Zealand children from 2017 to 2019.

OBJECTIVE: To examine whether the prevalence of age- and sex-adjusted BMI at, or above, the 85th, 95th and 99.7th percentiles continues to decline in New Zealand preschool children, over time. METHODS: As part of a national screening programme, 438,972 New Zealand 4-year-old children had their height and weight measured between 2011 and 2019. Age- and sex-adjusted BMI was calculated using WHO Growth Standards and the prevalence of children at, or above, the 85th, 95th, and 99.7th percentiles and at, or below, the 2nd percentile were determined. Log-binomial models were used to estimate linear time trends of ≥85th, ≥95th and ≥99.7th percentiles for the overall sample and separately by sex, deprivation, ethnicity and urban-rural classification. RESULTS: The percentage of children at, or above, the 85th, 95th and 99.7th percentile reduced by 4.9% [95% CI: 4.1%, 5.7%], 3.5% [95% CI: 2.9%, 4.1%], and 0.9% [95% CI: 0.7%, 1.2%], respectively, between '2011/12' and '2018/19'. There was evidence of a decreasing linear trend (risk reduction, per year) for the percentage of children ≥85th (risk ratio (RR): 0.980 [95% CI: 0.978, 0.982]), ≥95th (RR: 0.966 [95% CI: 0.962, 0.969]) and ≥99.7th (RR: 0.957 [95% CI: 0.950, 0.964]) percentiles. Downward trends were also evident across all socioeconomic indicators (sex, ethnicity, deprivation, and urban-rural classification), for each of the BMI thresholds. Larger absolute decreases were evident for children residing in the most deprived compared with the least deprived areas, at each BMI threshold. There appeared to be no consistent trend for the percentage of children ≤2nd percentile. CONCLUSIONS: Reassuringly, continued declines of children with age- and sex-adjusted BMI at, or above, the 85th, 95th and 99.7th percentiles are occurring over time, overall and across all sociodemographic indicators, with little evidence for consistent trends in the prevalence of children at, or below, the 2nd percentile.

Infant Sleep Hazards and the Risk of Sudden Unexpected Death in Infancy.

OBJECTIVE: To examine the effects of infant sofa-sleeping, recent use by caregivers of alcohol, cannabis, and/or other drugs, and bed type and pillows, on the risk of sudden unexpected death in infancy (SUDI) in New Zealand. STUDY DESIGN: A nationwide prospective case-control study was implemented between March 2012 and February 2015. Data were collected during interviews with parents/caregivers. "Hazards" were defined as infant exposure to 1 or more of sofa-sleeping and recent use by caregivers of alcohol, cannabis, and other drugs. The interaction of hazards with tobacco smoking in pregnancy and bed sharing, including for very young infants, and the difference in risk for Maori and non-Maori infants, also were assessed. RESULTS: The study enrolled 132 cases and 258 controls. SUDI risk increased with infant sofa-sleeping (imputed aOR [IaOR] 24.22, 95% CI 1.65-356.40) and with hazards (IaOR 3.35, 95% CI 1.40-8.01). The SUDI risk from the combination of tobacco smoking in pregnancy and bed sharing (IaOR 29.0, 95% CI 10.10-83.33) increased with the addition of 1 or more hazards (IaOR 148.24, 95% CI 15.72-1398), and infants younger than 3 months appeared to be at greater risk (IaOR 450.61, 95% CI 26.84-7593.14). CONCLUSIONS: Tobacco smoking in pregnancy and bed sharing remain the greatest SUDI risks for infants and risk increases further in the presence of sofa-sleeping or recent caregiver use of alcohol and/or cannabis and other drugs. Continued implementation of effective, appropriate programs for smoking cessation, safe sleep, and supplying safe sleep beds is required to reduce New Zealand SUDI rates and SUDI disparity among Maori.

The care of infants with rapid weight gain: Should we be doing more?

Rapid weight gain (RWG) during infancy is a known risk factor for later childhood obesity. It can be measured using a range of definitions across various time periods in the first 2 years of life. In recent years, some early childhood obesity prevention trials have included a focus on preventing RWG during infancy, with modest success. Overall, RWG during infancy remains common, yet little work has examined whether infants with this growth pattern should receive additional care when it is identified in health-care settings. In this viewpoint, we contend that RWG during infancy should be routinely screened for in health-care settings, and when identified, viewed as an opportunity for health-care professionals to instigate non-stigmatising discussions with families about RWG and general healthy practices for their infants. If families wish to engage, we suggest that six topics from early life obesity prevention studies (breastfeeding, formula feeding, complementary feeding, sleep, responsive parenting, and education around growth charts and monitoring) could form the foundations of conversations to help them establish and maintain healthy habits to support their infant's health and well-being and potentially lower the risk of later obesity. However, further work is needed to develop definitive guidelines in this area, and to address other gaps in the literature, such as the current lack of a standardised definition for RWG during infancy and a clear understanding of the time points over which it should be measured.

Nbn-Mre11 interaction is required for tumor suppression and genomic integrity.

We derived a mouse model in which a mutant form of Nbn/Nbs1mid8 (hereafter Nbnmid8) exhibits severely impaired binding to the Mre11-Rad50 core of the Mre11 complex. The Nbnmid8 allele was expressed exclusively in hematopoietic lineages (in Nbn-/mid8vav mice). Unlike Nbnflox/floxvav mice with Nbn deficiency in the bone marrow, Nbn-/mid8vav mice were viable. Nbn-/mid8vav mice hematopoiesis was profoundly defective, exhibiting reduced cellularity of thymus and bone marrow, and stage-specific blockage of B cell development. Within 6 mo, Nbn-/mid8 mice developed highly penetrant T cell leukemias. Nbn-/mid8vav leukemias recapitulated mutational features of human T cell acute lymphoblastic leukemia (T-ALL), containing mutations in NOTCH1, TP53, BCL6, BCOR, and IKZF1, suggesting that Nbnmid8 mice may provide a venue to examine the relationship between the Mre11 complex and oncogene activation in the hematopoietic compartment. Genomic analysis of Nbn-/mid8vav malignancies showed focal amplification of 9qA2, causing overexpression of MRE11 and CHK1 We propose that overexpression of MRE11 compensates for the metastable Mre11-Nbnmid8 interaction, and that selective pressure for overexpression reflects the essential role of Nbn in promoting assembly and activity of the Mre11 complex.

Convergent genetic aberrations in murine and human T lineage acute lymphoblastic leukemias.

The lack of predictive preclinical models is a fundamental barrier to translating knowledge about the molecular pathogenesis of cancer into improved therapies. Insertional mutagenesis (IM) in mice is a robust strategy for generating malignancies that recapitulate the extensive inter- and intra-tumoral genetic heterogeneity found in advanced human cancers. While the central role of "driver" viral insertions in IM models that aberrantly increase the expression of proto-oncogenes or disrupt tumor suppressors has been appreciated for many years, the contributions of cooperating somatic mutations and large chromosomal alterations to tumorigenesis are largely unknown. Integrated genomic studies of T lineage acute lymphoblastic leukemias (T-ALLs) generated by IM in wild-type (WT) and Kras mutant mice reveal frequent point mutations and other recurrent non-insertional genetic alterations that also occur in human T-ALL. These somatic mutations are sensitive and specific markers for defining clonal dynamics and identifying candidate resistance mechanisms in leukemias that relapse after an initial therapeutic response. Primary cancers initiated by IM and resistant clones that emerge during in vivo treatment close key gaps in existing preclinical models, and are robust platforms for investigating the efficacy of new therapies and for elucidating how drug exposure shapes tumor evolution and patterns of resistance.