Alveolar Differentiation Drives Resistance to KRAS Inhibition in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD), commonly driven by KRAS mutations, is responsible for 7% of all cancer mortality. The first allele-specific KRAS inhibitors were recently approved in LUAD, but the clinical benefit is limited by intrinsic and acquired resistance. LUAD predominantly arises from alveolar type 2 (AT2) cells, which function as facultative alveolar stem cells by self-renewing and replacing alveolar type 1 (AT1) cells. Using genetically engineered mouse models, patient-derived xenografts, and patient samples, we found inhibition of KRAS promotes transition to a quiescent AT1-like cancer cell state in LUAD tumors. Similarly, suppressing Kras induced AT1 differentiation of wild-type AT2 cells upon lung injury. The AT1-like LUAD cells exhibited high growth and differentiation potential upon treatment cessation, whereas ablation of the AT1-like cells robustly improved treatment response to KRAS inhibitors. Our results uncover an unexpected role for KRAS in promoting intratumoral heterogeneity and suggest that targeting alveolar differentiation may augment KRAS-targeted therapies in LUAD.

SIGNIFICANCE

Treatment resistance limits response to KRAS inhibitors in LUAD patients. We find LUAD residual disease following KRAS targeting is composed of AT1-like cancer cells with the capacity to reignite tumorigenesis. Targeting the AT1-like cells augments responses to KRAS inhibition, elucidating a therapeutic strategy to overcome resistance to KRAS-targeted therapy. This article is featured in Selected Articles from This Issue, p. 201.

Tenascin-C expressing touch dome keratinocytes exhibit characteristics of all epidermal lineages

The touch dome (TD) keratinocytes are specialized epidermal cells that intimately associate with the light touch sensing Merkel cells (MCs). The TD keratinocytes function as a niche for the MCs and can induce de novo hair follicles upon stimulation; however, how the TD keratinocytes are maintained during homeostasis remains unclear. scRNA-seq identified a specific TD keratinocyte marker, Tenascin-C (TNC). Lineage tracing of Tnc-expressing TD keratinocytes revealed that these cells maintain themselves as an autonomous epidermal compartment and give rise to MCs upon injury. Molecular characterization uncovered that, while the transcriptional and chromatin landscape of the TD keratinocytes is remarkably similar to that of the interfollicular epidermal keratinocytes, it also shares certain molecular signatures with the hair follicle keratinocytes. Our study highlights that the TD keratinocytes in the adult skin have molecular characteristics of keratinocytes of diverse epidermal lineages.

Alveolar differentiation drives resistance to KRAS inhibition in lung adenocarcinoma

Lung adenocarcinoma (LUAD), commonly driven by KRAS mutations, is responsible for 7% of all cancer mortality. The first allele-specific KRAS inhibitors were recently approved in LUAD, but clinical benefit is limited by intrinsic and acquired resistance. LUAD predominantly arises from alveolar type 2 (AT2) cells, which function as facultative alveolar stem cells by self-renewing and replacing alveolar type 1 (AT1) cells. Using genetically engineered mouse models, patient-derived xenografts, and patient samples we found inhibition of KRAS promotes transition to a quiescent AT1-like cancer cell state in LUAD tumors. Similarly, suppressing Kras induced AT1 differentiation of wild-type AT2 cells upon lung injury. The AT1-like LUAD cells exhibited high growth and differentiation potential upon treatment cessation, whereas ablation of the AT1-like cells robustly improved treatment response to KRAS inhibitors. Our results uncover an unexpected role for KRAS in promoting intra-tumoral heterogeneity and suggest targeting alveolar differentiation may augment KRAS-targeted therapies in LUAD.

Significance

Treatment resistance limits response to KRAS inhibitors in LUAD patients. We find LUAD residual disease following KRAS targeting is composed of AT1-like cancer cells with the capacity to reignite tumorigenesis. Targeting the AT1-like cells augments responses to KRAS inhibition, elucidating a therapeutic strategy to overcome resistance to KRAS-targeted therapy.

Abstract PR010: Aging-induced reprogramming of the cell of origin defines lung cancer evolution

Aging is one of the most important risk factors for cancer development. However, our understanding of how aging impacts cancer evolution remains at an early stage. We investigated the evolution of lung adenocarcinoma (LUAD) in aged vs. young KrasLSL-G12D/+; Trp53flox/flox (KP) mice. Surprisingly, we found that LUAD initiation and progression were significantly impaired with aging. Using functional in vivo and in vitro assays, we demonstrated that the loss of tumor-initiating potential could be attributed to a loss of stemness in the alveolar type 2 (AT2) cells, which are the predominant cell of origin for LUAD. We next explored the biology of the tumors that formed in aged KP mice using single-cell transcriptomics. We discovered a distinct compositional landscape of cancer cell subsets in aged lung tumors, revealing a delay in the molecular progression of the cancers and an aging-specific gene expression signature. Interestingly, key components of this gene signature could be traced back to specific epigenetic alterations in the AT2 cells. Furthermore, the aged mouse LUAD signature was highly predictive of patient age in human LUAD, indicating conservation of the age-associated changes across species. We hypothesized that the aging-associated changes in gene expression during LUAD tumorigenesis may underpin delayed tumor progression in the aged KP mice. To test this, we performed an in vivo genetic screen in the autochthonous KP model and identified genetic dependencies that were specific to LUAD in aged or young mice. Our results indicate that aging-associated epigenetic changes in the cell of origin are imprinted on evolving tumors, which determines tumor initiation potential, alters trajectory of tumor evolution, and leads to age-dependent vulnerabilities. These findings suggest that the biology of tumors is fundamentally altered by aging, raising new possibilities for cancer treatment and prevention in patients of different ages.

Citation Format: Xueqian Zhuang, Simon Joost, Qing Wang, Melissa Blum, Selena Ding, Zhuxuan Li, Yingqian Zhan, Richard Koche, Emily Wong, Tuomas Tammela. Aging-induced reprogramming of the cell of origin defines lung cancer evolution [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr PR010.

Abstract B019: Aging-induced reprogramming of the cell of origin defines lung cancer evolution

This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Short Talks from Proffered Abstracts section (PR010) of the Conference Proceedings.

Citation Format: Xueqian Zhuang, Simon Joost, Qing Wang, Melissa Blum, Selena Ding, Zhuxuan Li, Yingqian Zhan, Richard Koche, Emily Wong, Tuomas Tammela. Aging-induced reprogramming of the cell of origin defines lung cancer evolution [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr B019.

Plasticity of Epithelial Cells during Skin Wound Healing

Epithelial tissues line the outer surfaces of the mammalian body and protect from external harm. In skin, the epithelium is maintained by distinct stem cell populations residing in the interfollicular epidermis and various niches of the hair follicle. These stem cells give rise to the stratified epidermal layers and the protective hair coat, while being confined to their respective niches. Upon injury, however, all stem cell progenies can leave their niche and collectively contribute to a central wound healing process, called reepithelialization, for restoring the skin's barrier function. This review explores how epithelial cells from distinct niches respond and adapt during acute wound repair. We discuss when and where cells sense and react to damage, how cellular identity is regulated at the molecular and behavioral level, and how cells memorize past experiences and their origin. This collective knowledge highlights cellular plasticity as a brilliant feature of epithelial tissues to heal.

Systematic Comparison of Pancreatic Ductal Adenocarcinoma Models Identifies a Conserved Highly Plastic Basal Cell State

Intratumoral heterogeneity and cellular plasticity have emerged as hallmarks of cancer, including pancreatic ductal adenocarcinoma (PDAC). As PDAC portends a dire prognosis, a better understanding of the mechanisms underpinning cellular diversity in PDAC is crucial. Here, we investigated the cellular heterogeneity of PDAC cancer cells across a range of in vitro and in vivo growth conditions using single-cell genomics. Heterogeneity contracted significantly in two-dimensional and three-dimensional cell culture models but was restored upon orthotopic transplantation. Orthotopic transplants reproducibly acquired cell states identified in autochthonous PDAC tumors, including a basal state exhibiting coexpression and coaccessibility of epithelial and mesenchymal genes. Lineage tracing combined with single-cell transcriptomics revealed that basal cells display high plasticity in situ. This work defines the impact of cellular growth conditions on phenotypic diversity and uncovers a highly plastic cell state with the capacity to facilitate state transitions and promote intratumoral heterogeneity in PDAC.

SIGNIFICANCE

This work provides important insights into how different model systems of pancreatic ductal adenocarcinoma mold the phenotypic space of cancer cells, highlighting the power of in vivo models.

Development of a web-platform for dynamic monitoring of population health in Geneva: Specchio project

Background

In order to provide efficient public health decisions making, it is crucial to obtain reliable and recent data on the state of health of the population. For that purpose, a web-platform for the dynamic monitoring of the health status and well-being of the population is being developed in the Geneva canton.

Methods

Using a dedicated website, recruitment will be carried out over 5 years so as to enroll up to 20 000 volunteers, resident in Geneva and aged ≥ 18 years, followed-up for at least 10 years. Once connected to the website, participants will fill a general self-administered questionnaire on their socio-demographic and lifestyle characteristics, anthropometry, health status, physical activity and diet. Environmental, behavioral and occupational exposures will also be evaluated via more specific questionnaires. Current addresses of residence will be geocoded and linked to geographical databases to passively gather information on noise, air pollution, green areas, and other exposures. Surveillance of health events will be implemented via yearly self-administered on line questionnaires and potentially via passive linkage to medical databases (medical file) and health registries with the participants' consent. For a subsample of volunteers, biochemical samples and biomarkers will be collected.

Results

The pilot study shows that the project is feasible, potentially cost-effective but requires innovative methodologies for ensuring long term follow-up. Different communication strategies used for recruitment and long-term participation need to be implemented ensuring trust from participants, different levels of health literacy and the need of justice.

Conclusions

Specchio is a new project aimed at setting up a digital longitudinal health study in Geneva. Challenges concerns the determinants of participation, recruitment and attrition, quality of data and ethics. Long-term funding by the Directorate General of Health Geneva is currently under evaluation.

Key messages

This digital longitudinal health study will enable dynamic monitoring of the health status and well-being of Geneva residents and will enable efficient public health decision making. Specchio is a new project funded by the Directorate General of Health Geneva.

Coordinated hedgehog signaling induces new hair follicles in adult skin

Hair follicle (HF) development is orchestrated by coordinated signals from adjacent epithelial and mesenchymal cells. In humans this process only occurs during embryogenesis and viable strategies to induce new HFs in adult skin are lacking. Here, we reveal that activation of Hedgehog (Hh) signaling in adjacent epithelial and stromal cells induces new HFs in adult, unwounded dorsal mouse skin. Formation of de novo HFs recapitulated embryonic HF development, and mature follicles produced hair co-occurring with epithelial tumors. In contrast, Hh-pathway activation in epithelial or stromal cells alone resulted in tumor formation or stromal cell condensation respectively, without induction of new HFs. Provocatively, adjacent epithelial-stromal Hh-pathway activation induced de novo HFs also in hairless paw skin, divorced from confounding effects of pre-existing niche signals in haired skin. Altogether, cell-type-specific modulation of a single pathway is sufficient to reactivate embryonic programs in adult tissues, thereby inducing complex epithelial structures even without wounding.

We are born with all the hair follicles that we will ever have in our life. These structures are maintained by different types of cells (such as keratinocytes and fibroblasts) that work together to create hair. Follicles form in the embryo thanks to complex molecular signals, which include a molecular cascade known as the Hedgehog signaling pathway.

After birth however, these molecular signals are shut down to avoid conflicting messages – inappropriate activation of Hedgehog signaling in adult skin, for instance, leads to tumors. This means that our skin loses the ability to make new hair follicles, and if skin is severely damaged it cannot regrow hair or produce the associated sebaceous glands that keep skin moisturized.

Being able to create new hair follicles in adult skin would be both functionally and aesthetically beneficial for patients in need, for example, burn victims. Overall, it would also help to understand if and how it is possible to reactivate developmental programs after birth.

To investigate this question, Sun, Are et al. triggered Hedgehog signaling in the skin cells of genetically modified mice; this was done either in keratinocytes, in fibroblasts, or in both types of cells. The experiments showed that Hedgehog signaling could produce new hair follicles, but only when activated in keratinocytes and fibroblasts together. The process took several weeks, mirrored normal hair follicle development and resulted in new hair shafts. The follicles grew on both the back of mice, where hair normally occurs, and even in paw areas that are usually hairless.

Not unexpectedly the new hair follicles were accompanied with skin tumors. But, promisingly, treatment with Hedgehog-pathway inhibitor Vismodegib restricted tumor growth while keeping the new follicles intact. This suggests that future work on improving “when and where” Hedgehog signaling is activated may allow the formation of new follicles in adult skin with fewer adverse effects.

The Molecular Anatomy of Mouse Skin during Hair Growth and Rest

Skin homeostasis is orchestrated by dozens of cell types that together direct stem cell renewal, lineage commitment, and differentiation. Here, we use single-cell RNA sequencing and single-molecule RNA FISH to provide a systematic molecular atlas of full-thickness skin, determining gene expression profiles and spatial locations that define 56 cell types and states during hair growth and rest. These findings reveal how the outer root sheath (ORS) and inner hair follicle layers coordinate hair production. We found that the ORS is composed of two intermingling but transcriptionally distinct cell types with differing capacities for interactions with stromal cell types. Inner layer cells branch from transcriptionally uncommitted progenitors, and each lineage differentiation passes through an intermediate state. We also provide an online tool to explore this comprehensive skin cell atlas, including epithelial and stromal cells such as fibroblasts, vascular, and immune cells, to spur further discoveries in skin biology.

Individual-level high definition spatial distribution of mammography uptake in Geneva (Switzerland)

Background

The local social and physical environment influences health outcomes and individual behaviour. It remains unknown if the environmental influence is independent of individual socioeconomic status (SES). We studied the spatial distribution of mammography screening uptake in the Swiss urban population of Geneva and determined its independence from SES.

Methods

We used individual-level geo-referenced data (n = 5 002) from the participants in the Bus Santé study, a population-based cross-sectional study ongoing in Geneva since 1992. Data from 1992 to 2014 have been included in this study. Local indicators of spatial association (LISA) were calculated and used to assess the spatial dependence of mammography uptake (defined as having had a mammography in the past). We report unadjusted spatial clusters; adjusted for neighbourhood income and individual educational attainment; and for demographic variables (age and Swiss nationality). Furthermore, we evaluated the association between the distance to the nearest screening centre and the identified spatial clusters.

Results

Mammography uptake was not randomly distributed, with spatial clusters overlapping with those of SES. Spatial clusters were reduced to 56.2% of their initial size (n = 1,033) after adjustment for SES variables. Adjustment for age and nationality further reduced the proportion of individuals exhibiting spatially-dependent behaviour (to 36.5% of the initial size). Distance to the nearest screening centre was not associated with the spatial distribution of mammography uptake.

Conclusions

High definition spatial distribution studies using analysis of individual data allow identifying spatial clusters which are not based on pre-determined administrative units (e.g. postal code) but rather on individual behaviour. Persistent spatial clusters after adjustment for SES and demographic confounders suggest additional area-level determinants influencing the spatial distribution of mammography uptake.

Key messages

High definition spatial studies can help uncover new patterns of health outcomes distribution independent of SES and based on individual behaviour, rather than administrative units. While SES explains a great proportion of the spatial distribution of mammography uptake, other still elusive factors may be contributing to the observed spatial inequalities in mammography uptake.

Indication of spatially random occurrence of Chlamydia-like organisms in Bufo bufo tadpoles from ponds located in the Geneva metropolitan area

Occurrence of bacteria belonging to the order Chlamydiales was investigated for the first time in common toad (Bufo bufo) tadpole populations collected from 41 ponds in the Geneva metropolitan area, Switzerland. A Chlamydiales-specific real-time PCR was used to detect and amplify the Chlamydiales 16S ribosomal RNA–encoding gene from the tails of 375 tadpoles. We found the studied amphibian populations to host Chlamydia-like organisms (CLOs) attributable to the genera Similichlamydia, Neochlamydia, Protochlamydia and Parachlamydia (all belonging to the family Parachlamydiaceae), Simkania (family Simkaniaceae) and Estrella (family Criblamydiaceae); additionally, DNA from the genus Thermoanaerobacter (family Thermoanaerobacteriaceae) was detected. Global autocorrelation analysis did not reveal a spatial structure in the observed CLOs occurrence rates, and association tests involving land cover characteristics did not evidence any clear effect on CLOs occurrence rates in B. bufo. Although preliminary, these results suggest a random and ubiquitous distribution of CLOs in the environment, which would support the biogeographical expectation ‘everything is everywhere’ for the concerned microorganisms.

Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population

Regulation of adipose tissue stem cells (ASCs) and adipogenesis impact the development of excess body fat-related metabolic complications. Animal studies have suggested the presence of distinct subtypes of ASCs with different differentiation properties. In addition, ASCs are becoming the biggest source of mesenchymal stem cells used in therapies, which requires deep characterization. Using unbiased single cell transcriptomics we aimed to characterize ASC populations in human subcutaneous white adipose tissue (scWAT). The transcriptomes of 574 single cells from the WAT total stroma vascular fraction (SVF) of four healthy women were analyzed by clustering and t-distributed stochastic neighbor embedding visualization. The identified cell populations were then mapped to cell types present in WAT using data from gene expression microarray profiling of flow cytometry-sorted SVF. Cells clustered into four distinct populations: three adipose tissue-resident macrophage subtypes and one large, homogeneous population of ASCs. While pseudotemporal ordering analysis indicated that the ASCs were in slightly different differentiation stages, the differences in gene expression were small and could not distinguish distinct ASC subtypes. Altogether, in healthy individuals, ASCs seem to constitute a single homogeneous cell population that cannot be subdivided by single cell transcriptomics, suggesting a common origin for human adipocytes in scWAT.

Persistence of butterfly populations in fragmented habitats along urban density gradients: motility helps

In a simulation study of genotypes conducted over 100 generations for more than 1600 butterfly's individuals, we evaluate how the increase of anthropogenic fragmentation and reduction of habitat size along urbanisation gradients (from 7 to 59% of impervious land cover) influences genetic diversity and population persistence in butterfly species. We show that in areas characterised by a high urbanisation rate (>56% impervious land cover), a large decrease of both genetic diversity (loss of 60-80% of initial observed heterozygosity) and population size (loss of 70-90% of individuals) is observed over time. This is confirmed by empirical data available for the mobile butterfly species Pieris rapae in a subpart of the study area. Comparing simulated data for P. rapae with its normal dispersal ability and with a reduced dispersal ability, we also show that a higher dispersal ability can be an advantage to survive in an urban or highly fragmented environment. The results obtained here suggest that it is of high importance to account for population persistence, and confirm that it is crucial to maintain habitat size and connectivity in the context of land-use planning.

High performance computation of landscape genomic models including local indicators of spatial association

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an F_ST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.

High performance computation of landscape genomic models including local indicators of spatial association

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an F_ST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

The murine epidermis with its hair follicles represents an invaluable model system for tissue regeneration and stem cell research. Here we used single-cell RNA-sequencing to reveal how cellular heterogeneity of murine telogen epidermis is tuned at the transcriptional level. Unbiased clustering of 1,422 single-cell transcriptomes revealed 25 distinct populations of interfollicular and follicular epidermal cells. Our data allowed the reconstruction of gene expression programs during epidermal differentiation and along the proximal-distal axis of the hair follicle at unprecedented resolution. Moreover, transcriptional heterogeneity of the epidermis can essentially be explained along these two axes, and we show that heterogeneity in stem cell compartments generally reflects this model: stem cell populations are segregated by spatial signatures but share a common basal-epidermal gene module. This study provides an unbiased and systematic view of transcriptional organization of adult epidermis and highlights how cellular heterogeneity can be orchestrated in vivo to assure tissue homeostasis.

•

Single-cell RNA-seq analysis identifies 25 populations of epidermal cells

•

Differentiation and spatial gene expression signatures can be defined

•

Interplay of differentiation and spatial signatures explains most heterogeneity

•

Stem cell populations are divided by spatial signatures and only share basal identity

Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth

A role for Hedgehog (Hh) signalling in the development of colorectal cancer (CRC) has been proposed. In CRC and other solid tumours, Hh ligands are upregulated; however, a specific Hh antagonist provided no benefit in a clinical trial. Here we use Hh reporter mice to show that downstream Hh activity is unexpectedly diminished in a mouse model of colitis-associated colon cancer, and that downstream Hh signalling is restricted to the stroma. Functionally, stroma-specific Hh activation in mice markedly reduces the tumour load and blocks progression of advanced neoplasms, partly via the modulation of BMP signalling and restriction of the colonic stem cell signature. By contrast, attenuated Hh signalling accelerates colonic tumourigenesis. In human CRC, downstream Hh activity is similarly reduced and canonical Hh signalling remains predominantly paracrine. Our results suggest that diminished downstream Hh signalling enhances CRC development, and that stromal Hh activation can act as a colonic tumour suppressor.

The Hedgehog signalling pathway can drive tumorigenesis. Here, the authors show that in a colitis-associated colon cancer model downstream Hedgehog signalling is restricted to the stroma and its over-activation can inhibit tumorigenesis, associated with activation of BMP signaling.

Dynamics of Lgr6⁺ Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis

The dynamics and interactions between stem cell pools in the hair follicle (HF), sebaceous gland (SG), and interfollicular epidermis (IFE) of murine skin are still poorly understood. In this study, we used multicolor lineage tracing to mark Lgr6⁺ -expressing basal cells in the HF isthmus, SG, and IFE.We show that these Lgr6⁺ cells constitute long-term self-renewing populations within each compartment in adult skin. Quantitative analysis of clonal dynamics revealed that the Lgr6⁺ progenitor cells compete neutrally in the IFE, isthmus, and SG, indicating population asymmetry as the underlying mode of tissue renewal. Transcriptional profiling of Lgr6⁺ and Lgr6⁺ cells did not reveal a distinct Lgr6⁺ -associated gene expression signature, raising the question of whether Lgr6⁺ expression requires extrinsic niche signals. Our results elucidate the interrelation and behavior of Lgr6⁺ populations in the IFE, HF, and SG and suggest population asymmetry as a common mechanism for homeostasis in several epithelial skin compartments.

A comparison of the spatial dependence of body mass index among adults and children in a Swiss general population

Background:

Body mass index (BMI) may cluster in space among adults and be spatially dependent. Whether BMI clusters among children and how age-specific BMI clusters are related remains unknown. We aimed to identify and compare the spatial dependence of BMI in adults and children in a Swiss general population, taking into account the area's income level.

Methods:

Geo-referenced data from the Bus Santé study (adults, n=6663) and Geneva School Health Service (children, n=3601) were used. We implemented global (Moran's I) and local (local indicators of spatial association (LISA)) indices of spatial autocorrelation to investigate the spatial dependence of BMI in adults (35–74 years) and children (6–7 years). Weight and height were measured using standardized procedures. Five spatial autocorrelation classes (LISA clusters) were defined including the high–high BMI class (high BMI participant's BMI value correlated with high BMI-neighbors' mean BMI values). The spatial distributions of clusters were compared between adults and children with and without adjustment for area's income level.

Results:

In both adults and children, BMI was clearly not distributed at random across the State of Geneva. Both adults' and children's BMIs were associated with the mean BMI of their neighborhood. We found that the clusters of higher BMI in adults and children are located in close, yet different, areas of the state. Significant clusters of high versus low BMIs were clearly identified in both adults and children. Area's income level was associated with children's BMI clusters.

Conclusions:

BMI clusters show a specific spatial dependence in adults and children from the general population. Using a fine-scale spatial analytic approach, we identified life course-specific clusters that could guide tailored interventions.

Quantitative single-cell RNA-seq with unique molecular identifiers

Single-cell RNA sequencing (RNA-seq) is a powerful tool to reveal cellular heterogeneity, discover new cell types and characterize tumor microevolution. However, losses in cDNA synthesis and bias in cDNA amplification lead to severe quantitative errors. We show that molecular labels--random sequences that label individual molecules--can nearly eliminate amplification noise, and that microfluidic sample preparation and optimized reagents produce a fivefold improvement in mRNA capture efficiency.

GLI1 inhibition promotes epithelial-to-mesenchymal transition in pancreatic cancer cells

The Hedgehog (HH) pathway has been identified as an important deregulated signal transduction pathway in pancreatic ductal adenocarcinoma (PDAC), a cancer type characterized by a highly metastatic phenotype. In PDAC, the canonical HH pathway activity is restricted to the stromal compartment while HH signaling in the tumor cells is reduced as a consequence of constitutive KRAS activation. Here, we report that in the tumor compartment of PDAC the HH pathway effector transcription factor GLI1 regulates epithelial differentiation. RNAi-mediated knockdown of GLI1 abolished characteristics of epithelial differentiation, increased cell motility, and synergized with TGFβ to induce an epithelial-to-mesenchymal transition (EMT). Notably, EMT conversion in PDAC cells occurred in the absence of induction of SNAIL or SLUG, two canonical inducers of EMT in many other settings. Further mechanistic analysis revealed that GLI1 directly regulated the transcription of E-cadherin, a key determinant of epithelial tissue organization. Collectively, our findings identify GLI1 as an important positive regulator of epithelial differentiation, and they offer an explanation for how decreased levels of GLI1 are likely to contribute to the highly metastatic phenotype of PDAC.

Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources

The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources

In livestock genetic resource conservation, decision making about conservation priorities is based on the simultaneous analysis of several different criteria that may contribute to long-term sustainable breeding conditions, such as genetic and demographic characteristics, environmental conditions, and role of the breed in the local or regional economy. Here we address methods to integrate different data sets and highlight problems related to interdisciplinary comparisons. Data integration is based on the use of geographic coordinates and Geographic Information Systems (GIS). In addition to technical problems related to projection systems, GIS have to face the challenging issue of the non homogeneous scale of their data sets. We give examples of the successful use of GIS for data integration and examine the risk of obtaining biased results when integrating datasets that have been captured at different scales.

A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation

The detection of adaptive loci in the genome is essential as it gives the possibility of understanding what proportion of a genome or which genes are being shaped by natural selection. Several statistical methods have been developed which make use of molecular data to reveal genomic regions under selection. In this paper, we propose an approach to address this issue from the environmental angle, in order to complement results obtained by population genetics. We introduce a new method to detect signatures of natural selection based on the application of spatial analysis, with the contribution of geographical information systems (GIS), environmental variables and molecular data. Multiple univariate logistic regressions were carried out to test for association between allelic frequencies at marker loci and environmental variables. This spatial analysis method (SAM) is similar to current population genomics approaches since it is designed to scan hundreds of markers to assess a putative association with hundreds of environmental variables. Here, by application to studies of pine weevils and breeds of sheep we demonstrate a strong correspondence between SAM results and those obtained using population genetics approaches. Statistical signals were found that associate loci with environmental parameters, and these loci behave atypically in comparison with the theoretical distribution for neutral loci. The contribution of this new tool is not only to permit the identification of loci under selection but also to establish hypotheses about ecological factors that could exert the selection pressure responsible. In the future, such an approach may accelerate the process of hunting for functional genes at the population level.

Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection

The discovery of SNPs was performed using animals from eight European sheep breeds. Eleven SNPs were further characterized using about 1,700 sheep belonging to 57 breeds. A method for the identification of loci that were likely subject to selection was applied; three of the 11 SNPs lying outside the 95% confidence region of the conditional joint distribution of F(ST) and mean heterozygosity were identified as outliers.

[Angelman syndrome]

An eight-year-old boy with Angelman-(Happy Puppet-)Syndrome is described. Nearly all typical symptoms of the syndrome, especially severe psychomotoric retardation with spontaneous outbursts of laughing and protrusions of the tongue, athetoid movements, typical electroencephalogram and microcephaly, could be found in our patient. The incidence of the Angelman-syndrome may be underestimated.