Gene networks reveal stem-cell state convergence during preneoplasia and progression to malignancy in multistage skin carcinogenesis

Adult mammalian stem cells play critical roles in normal tissue homeostasis, as well as in tumor development, by contributing to cell heterogeneity, plasticity, and development of drug resistance. The relationship between different types of normal and cancer stem cells is highly controversial and poorly understood. Here, we carried out gene expression network analysis of normal and tumor samples from genetically heterogeneous mice to create network metagenes for visualization of stem-cell networks, rather than individual stem-cell markers, at the single-cell level during multistage carcinogenesis. We combined this approach with lineage tracing and single-cell RNASeq of stem cells and their progeny, identifying a previously unrecognized hierarchy in which Lgr6+ stem cells from tumors generate progeny that express a range of other stem-cell markers including Sox2, Pitx1, Foxa1, Klf5, and Cd44. Our data identify a convergence of multiple stem-cell and tumor-suppressor pathways in benign tumor cells expressing markers of lineage plasticity and oxidative stress. This same single-cell population expresses network metagenes corresponding to markers of cancer drug resistance in human tumors of the skin, lung and prostate. Treatment of mouse squamous carcinomas in vivo with the chemotherapeutic cis-platin resulted in elevated expression of the genes that mark this cell population. Our data have allowed us to create a simplified model of multistage carcinogenesis that identifies distinct stem-cell states at different stages of tumor progression, thereby identifying networks involved in lineage plasticity, drug resistance, and immune surveillance, providing a rich source of potential targets for cancer therapy.

Abstract 2198: The impact of carcinogens, obesity, and chronic inflammatory processes on mutational signatures and cancer risk in mouse tumor models

An estimated 40% of all human cancers are suspected to be a result of modifiable risk factors such as obesity, high fat diet and chronic inflammation. Whole genome sequencing (WGS) of thousands of human tumors have revealed “mutational signatures” that provide a molecular footprint of cancer origins. Whether such signatures exist for modifiable cancer risk factors remains unclear. We studied the impact of lifestyle risk factors using a compendium of 107 mouse tumors that model obesity, high fat diet, wounding, chronic inflammation, or chemotherapy. We used a well-established 2-step skin carcinogenesis model composed of exposure to mutagen DMBA followed by tumor promoter TPA, generating squamous carcinomas that were analysed by WGS for identification of mutational signatures. In addition to recapitulating many COSMIC human signatures, we identified a novel SNV signature induced by a single treatment with DMBA (SBS.DMBA) which explains the majority of all detected mutations. While a single exposure of normal skin to DMBA induces a highly variable number of carcinogen-specific mutations, a very high mutation burden is insufficient for tumorigenesis. SNVs attributable to reactive oxygen species (ROS) are broadly found in about 25% of all mouse tumors, but are most prominent in tumors from mice that are exposed to DMBA in utero, suggesting that the developmental age of mutagen exposure may impact the repair of ROS generated mutations and that the timing of exposure is a poorly understudied component of carcinogenesis. In mouse tumor models of genetic and dietary obesity, the total mutational load and mutational signatures in tumors from obese mice were indistinguishable from those of lean mice despite dramatic differences in tumor latency and progression as well transcriptomic differences in immune activation. We found an enrichment in deleterious Tgfrb2 mutations in tumors from mice with low compared to high body mass index (BMI) (p<0.016). Using a conditionally activated RAS mouse model, we also show that a non-mutagenic inflammatory signal such as a chronic wound can act as the rate-limiting step for full tumor development. Surprisingly these tumors can be evoked even in somatic genomes with very few mutations apart from the initiating Ras driver. Finally, together with the Riva et al study, these chemically induced mouse tumors recapitulate >50% of established human cancer driver genes. DMBA caused 91% of all Hras/Kras mutations, but only a minority of other recurrent driver mutations in genes such as Trp53 and Tert, suggesting that these occur later during the process of carcinogenesis. Taken together, we have analyzed the largest compendium of WGS data from nearly 300 mouse tumors, showing that while exogenous promotional factors do not increase mutation burden or induce novel mutational patterns, they have a major rate-limiting role in determining cancer risk.

Citation Format: Yun Rose Li, Kyle Halliwill, Eve Kandyba, Reyno Delrosario, Quan Tran, Nora Bayani, Di Wu, Olga Mirzoeva, Melissa McCreery Reeves, Mishu Islam, Laura Riva, Eric Bergstrom, John Digiovanni, Ludmil Alexandrov, Allan Balmain. The impact of carcinogens, obesity, and chronic inflammatory processes on mutational signatures and cancer risk in mouse tumor models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2198.

Multicolour lineage tracing reveals clonal dynamics of squamous carcinoma evolution from initiation to metastasis

Tumor cells are subjected to evolutionary selection pressures during progression from initiation to metastasis. We analyzed the clonal evolution of squamous skin carcinomas induced by DMBA/TPA treatment using the K5CreER-Confetti mouse and stage-specific lineage tracing. We show that benign tumors are polyclonal, but only one population contains the Hras driver mutation. Benign papillomas are therefore monoclonal in origin, but recruit neighboring epithelial cells during growth. Papillomas that never progress to malignancy retain several distinct clones, whereas progression to carcinoma is associated with a clonal sweep. Newly generated clones within carcinomas demonstrate intratumoral invasion and clonal intermixing, often giving rise to metastases containing two or more distinct clones derived from the matched primary tumor. These data demonstrate that late stage tumor progression and dissemination are governed by evolutionary selection pressures that operate at a multicellular level, and thus differ from the clonal events that drive initiation and the benign-malignant transition.

Stimulation of hair follicle stem cell proliferation through an IL-1 dependent activation of γδT-cells

The cutaneous wound-healing program is a product of a complex interplay among diverse cell types within the skin. One fundamental process that is mediated by these reciprocal interactions is the mobilization of local stem cell pools to promote tissue regeneration and repair. Using the ablation of epidermal caspase-8 as a model of wound healing in Mus musculus, we analyzed the signaling components responsible for epithelial stem cell proliferation. We found that IL-1α and IL-7 secreted from keratinocytes work in tandem to expand the activated population of resident epidermal γδT-cells. A downstream effect of activated γδT-cells is the preferential proliferation of hair follicle stem cells. By contrast, IL-1α-dependent stimulation of dermal fibroblasts optimally stimulates epidermal stem cell proliferation. These findings provide new mechanistic insights into the regulation and function of epidermal cell–immune cell interactions and into how components that are classically associated with inflammation can differentially influence distinct stem cell niches within a tissue.

The skin is a physical barrier that protects the body from the outside world. If the skin is injured, the body mounts a “wound healing” response to rapidly mend and restore this protective barrier. Wound healing is a complex process and relies on the different types of cells in the skin communicating with each other.

Stem cells provide tissues, like the skin, with new cells. Normally, stem cells are in a resting or inactive state. Yet, during wound healing, stem cells near the injured area are awakened and start producing more cells to repair the wound. Understanding how stem cells become activated in a wound has proved challenging because only a small number of cells near a damaged site will respond, and it is difficult to distinguish their response from that of other cells slightly further away.

Now, Lee et al. overcome this hurdle by analyzing a genetically engineered mouse in which the entire skin displays a wound healing response, even without any injury or trauma. In these mice, most of the stem cells in the skin are awakened from their normal resting state and behave as if there is a wound to heal.

It turns out that a protein called interleukin-1, which is released from damaged skin cells known as keratinocytes, can activate two different groups of stem cells in the skin to help repair the injured tissue. One group lives in the hair follicle and is normally responsible for replacing the hair that falls from the body. Lee et al. found that when the skin is wounded interleukin-1 activates certain immune cells (called γδT-cells). These immune cells then awaken the resting stem cells in the hair follicle to multiply and travel to the wound site to repair the injury. The other group of stem cells resides in the outermost layer of the skin. Interleukin-1 can also activate so-called fibroblast cells, which then stimulate this second group of stem cells to divide and cover the open wound.

Quickly healing wounds has many health benefits such as preventing infection and shortening the time to recover from an injury. These new findings may help to repair injured skin in diseases such as diabetes, where wounds can take months to heal and often leads to permanent tissue damage. The next challenge is to identify the cues that instruct the stem cells to travel to the wound site and turn into the specific cells that are required to replace the damaged cells.

Lgr6 is a stem cell marker in mouse skin squamous cell carcinoma

The G-protein-coupled receptors Lgr4/5/6 are Wnt signalling mediators, but their functions in squamous carcinomas (SCCs) are unclear. Using lineage tracing in Lgr5-EGFP-CreERT2- and Lgr6-EGFP-CreERT2- Rosa26/Tomato reporter mice, we demonstrate that Lgr6, but not Lgr5, acts as an epithelial stem cell marker in vivo in SCCs. We identify, by single molecule in situ hybridisation and cell sorting, rare Lgr6-positive cells in immortalised keratinocytes, and show that their frequency increases in advanced SCCs. Lgr6 expression is enriched in cells with stem cell characteristics, and Lgr6 downregulation in vivo causes increased epidermal proliferation, with expanded lineage tracing from Lgr6⁺ epidermal stem cells. Surprisingly, Lgr6 germline knockout mice are predisposed to SCC development, by a mechanism that includes compensatory upregulation of Lgr5. These data provide a model for human patients with germline loss of function mutations in WNT pathway genes RSPO1 or LGR4, who show increased susceptibility to squamous tumour development.

A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning

The control principles behind robust cyclic regeneration of hair follicles (HFs) remain unclear. Using multi-scale modeling, we show that coupling inhibitors and activators with physical growth of HFs is sufficient to drive periodicity and excitability of hair regeneration. Model simulations and experimental data reveal that mouse skin behaves as a heterogeneous regenerative field, composed of anatomical domains where HFs have distinct cycling dynamics. Interactions between fast-cycling chin and ventral HFs and slow-cycling dorsal HFs produce bilaterally symmetric patterns. Ear skin behaves as a hyper-refractory domain with HFs in extended rest phase. Such hyper-refractivity relates to high levels of BMP ligands and WNT antagonists, in part expressed by ear-specific cartilage and muscle. Hair growth stops at the boundaries with hyper-refractory ears and anatomically discontinuous eyelids, generating wave-breaking effects. We posit that similar mechanisms for coupled regeneration with dominant activator, hyper-refractory, and wave-breaker regions can operate in other actively renewing organs.

Gene Expression Architecture of Mouse Dorsal and Tail Skin Reveals Functional Differences in Inflammation and Cancer

Inherited germline polymorphisms can cause gene expression levels in normal tissues to differ substantially between individuals. We present an analysis of the genetic architecture of normal adult skin from 470 genetically unique mice, demonstrating the effect of germline variants, skin tissue location, and perturbation by exogenous inflammation or tumorigenesis on gene signaling pathways. Gene networks related to specific cell types and signaling pathways, including sonic hedgehog (Shh), Wnt, Lgr family stem cell markers, and keratins, differed at these tissue sites, suggesting mechanisms for the differential susceptibility of dorsal and tail skin to development of skin diseases and tumorigenesis. The Pten tumor suppressor gene network is rewired in premalignant tumors compared to normal tissue, but this response to perturbation is lost during malignant progression. We present a software package for expression quantitative trait loci (eQTL) network analysis and demonstrate how network analysis of whole tissues provides insights into interactions between cell compartments and signaling molecules.

Defining the localization and molecular characteristic of minor salivary gland label-retaining cells

Adult stem cells (SCs) are important to maintain homeostasis of tissues including several mini-organs like hair follicles and sweat glands. However, the existence of stem cells in minor salivary glands (SGs) is largely unexplored. In vivo histone2B green fluorescent protein pulse chase strategy has allowed us to identify slow-cycling, label-retaining cells (LRCs) of minor SGs that preferentially localize in the basal layer of the lower excretory duct with a few in the acini. Engraftment of isolated SG LRC in vivo demonstrated their potential to differentiate into keratin 5 (basal layer marker) and keratin 8 (luminal layer marker)-positive structures. Transcriptional analysis revealed activation of TGFβ1 target genes in SG LRC and BMP signaling in SG progenitors. We also provide evidence that minor SGSCs are sensitive to tobacco-derived tumor-inducing agent and give rise to tumors resembling low grade adenoma. Our data highlight for the first time the existence of minor SG LRCs with stem cells characteristic and emphasize the role of transforming growth factor beta (TGFβ) pathway in their maintenance.

Wnt7b is an important intrinsic regulator of hair follicle stem cell homeostasis and hair follicle cycling

The hair follicle (HF) is an exceptional mini-organ to study the mechanisms which regulate HF morphogenesis, cycling, hair follicle stem cell (hfSCs) homeostasis, and progeny differentiation. During morphogenesis, Wnt signaling is well-characterized in the initiation of HF patterning but less is known about which particular Wnt ligands are required and whether individual Wnt ligands act in an indispensable or redundant manner during postnatal hfSCs anagen onset and HF cycle progression. Previously, we described the function of the bone morphogenetic protein (BMP) signaling target gene WNT7a in intrinsic regulation of hfSCs homeostasis in vivo. Here, we investigated the role of Wnt7b, which was also intrinsically upregulated in hfSCs during physiological and precocious anagen after BMP inhibition in vivo. We demonstrated Wnt7b to be a direct target of canonical BMP signaling in hfSCs and using Wnt7b conditional gene targeting during HF morphogenesis revealed disrupted HF cycling including a shorter anagen, premature catagen onset with overall shorter hair production, and diminished HF differentiation marker expression. Additionally, we observed that postnatal ablation of Wnt7b resulted in delayed HF activation, affecting both the hair germ and bulge hfSCs but still maintaining a two-step sequence of HF stimulation. Interestingly, Wnt7b cKO hfSCs participated in reformation of the new HF bulge, but with slower self-renewal. These findings demonstrate the importance of intrinsic Wnt7b expression in hfSCs regulation and normal HF cycling and surprisingly reveal a nonredundant role for Wnt7b in the control of HF anagen length and catagen entry which was not compensated by other Wnt ligands.

Smad1 and 5 but not Smad8 establish stem cell quiescence which is critical to transform the premature hair follicle during morphogenesis toward the postnatal state

Hair follicles (HFs) are regenerative miniorgans that offer a highly informative model system to study the regulatory mechanisms of hair follicle stem cells (hfSCs) homeostasis and differentiation. Bone morphogenetic protein (BMP) signaling is key in both of these processes, governing hfSCs quiescence in the bulge and differentiation of matrix progenitors. However, whether canonical or noncanonical pathways of BMP signaling are responsible for these processes remains unresolved. Here, we conditionally ablated two canonical effectors of BMP signaling, Smad1 and Smad5 during hair morphogenesis and postnatal cycling in mouse skin. Deletion of Smad1 and Smad5 (dKO) in the epidermis during morphogenesis resulted in neonatal lethality with lack of visible whiskers. Interestingly, distinct patterns of phospho-Smads (pSmads) activation were detected with pSmad8 restricted to epidermis and pSmad1 and pSmad5 exclusively activated in HFs. Engraftment of dKO skin revealed retarded hair morphogenesis and failure to differentiate into visible hair. The formation of the prebulge and bulge reservoir for quiescent hfSCs was precluded in dKO HFs which remained in prolonged anagen. Surprisingly, in postnatal telogen HFs, pSmad8 expression was no longer limited to epidermis and was also present in dKO bulge hfSCs and matrix progenitors. Although pSmad8 activity alone could not prevent dKO hfSCs precocious anagen activation, it sustained efficient postnatal differentiation and regeneration of visible hairs. Together, our data suggest a pivotal role for canonical BMP signaling demonstrating distinguished nonoverlapping function of pSmad8 with pSmad1 and pSmad5 in hfSCs regulation and hair morphogenesis but a redundant role in adult hair progenitors differentiation.