An atlas of epithelial cell states and plasticity in lung adenocarcinoma.

Understanding the cellular processes that underlie early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies1. Here we studied 246,102 single epithelial cells from 16 early-stage LUADs and 47 matched normal lung samples. Epithelial cells comprised diverse normal and cancer cell states, and diversity among cancer cells was strongly linked to LUAD-specific oncogenic drivers. KRAS mutant cancer cells showed distinct transcriptional features, reduced differentiation and low levels of aneuploidy. Non-malignant areas surrounding human LUAD samples were enriched with alveolar intermediate cells that displayed elevated KRT8 expression (termed KRT8+ alveolar intermediate cells (KACs) here), reduced differentiation, increased plasticity and driver KRAS mutations. Expression profiles of KACs were enriched in lung precancer cells and in LUAD cells and signified poor survival. In mice exposed to tobacco carcinogen, KACs emerged before lung tumours and persisted for months after cessation of carcinogen exposure. Moreover, they acquired Kras mutations and conveyed sensitivity to targeted KRAS inhibition in KAC-enriched organoids derived from alveolar type 2 (AT2) cells. Last, lineage-labelling of AT2 cells or KRT8+ cells following carcinogen exposure showed that KACs are possible intermediates in AT2-to-tumour cell transformation. This study provides new insights into epithelial cell states at the root of LUAD development, and such states could harbour potential targets for prevention or intervention.

A spatially resolved single-cell genomic atlas of the adult human breast.

The adult human breast is comprised of an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue1-3. Although most previous studies have focused on the breast epithelial system4-6, many of the non-epithelial cell types remain understudied. Here we constructed the comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution. Our single-cell transcriptomics study profiled 714,331 cells from 126 women, and 117,346 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states. These data reveal abundant perivascular, endothelial and immune cell populations, and highly diverse luminal epithelial cell states. Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions. Collectively, these data provide a reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

Selective photodynamic effects on cervical adenocarcinoma cells provided by F127 Pluronic®-based micelles modulating hypericin delivery

Abstract Cervical cancer is a leading cause of death among women. The endocervical adenocarcinoma (ECA) represents an aggressive and metastatic type of cancer with no effective treatment options currently available. We evaluated the antitumoral and anti-migratory effects of hypericin (HYP) encapsulated on Pluronic F127 (F127/HYP) photodynamic therapy (PDT) against a human cell line derived from invasive cervical adenocarcinoma (HeLa) compared to a human epithelial cell line (HaCaT). The phototoxicity and cytotoxicity of F127/HYP were evaluated by the following assays: colorimetric assay, MTT, cellular morphological changes by microscopy and long-term cytotoxicity by clonogenic assay. In addition, we performed fluorescence microscopy to analyze cell uptake and subcellular distribution of F127/HYP, cell death pathway and reactive oxygen species (ROS) production. The PDT mechanism was determined with sodium azide and D-mannitol and cell migration by wound-healing assay. The treatment with F127/HYP promoted a phototoxic result in the HeLa cells in a dose-dependent and selective form. Internalization of F127/HYP was observed mainly in the mitochondria, causing cell death by necrosis and ROS production especially by the type II PDT mechanism. Furthermore, F127/HYP reduced the long-term proliferation and migration capacity of HeLa cells. Overall, our results indicate a potentially application of F127/HYP micelles as a novel approach for PDT with HYP delivery to more specifically treat ECA.

Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states.

Prostate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we perform single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients. We uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer and identify a population of tumor-associated club cells that may be associated with prostate carcinogenesis. ERG-negative tumor cells, compared to ERG-positive cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids harbor tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues. Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

Proteomic analysis of human keratinocytes under UVA-induced stress / Análise proteômica de queratinócitos humanos sob estresse induzido por luz UVA

The solar ultraviolet (UV) radiation that reaches the Earth is composed of 95% of UVA (320 to 400 nm) and 5% of UVB (280 to 320 nm) radiation. UVB is carcinogenic, generating potentially mutagenic DNA lesions. The solar UVA radiation also causes DNA damage, but this fact does not fully account for its biological impact. UVA is absorbed by non-DNA cellular chromophores, generating reactive oxygen species such as singlet oxygen. Knowing the proteome mediates stress responses in cells, here we investigated the cellular effects of a non-cytotoxic dose of UVA radiation, equivalent to about 20 minutes of midday sun exposure, on the proteome of human keratinocytes. Using a combination of mass spectrometry-based proteomics, bioinformatics, and conventional biochemical assays, we analyzed two aspects of UVA-induced stress: spatial remodeling of the proteome in subcellular compartments 30 minutes after stress and long-term changes in protein levels and secretion (24 hours and 7 days postirradiation). In the first part of this thesis, we quantified and assigned subcellular localization for over 3000 proteins, of which about 600 potentially redistribute upon UVA exposure. Protein redistributions were accompanied by redox modulations, mitochondrial fragmentation and DNA damage. In the second part of the work, our results showed that primary human keratinocytes enter senescence upon exposure to a single dose of UVA, mounting antioxidant and inflammatory responses. Cells under UVA-induced senescence further elicit paracrine responses in neighboring premalignant HaCaT epithelial cells via inflammatory mediators. Altogether, these results reiterate the role of UVA radiation as a potent metabolic stressor in the skin

A radiação ultravioleta (UV) solar que atinge a superfície terrestre é composta por 95% de radiação UVA (320 a 400 nm) e 5% de radiação UVB (280 a 320 nm). A radiação UVB é carcinogênica e gera lesões potencialmente mutagênicas no DNA. A radiação UVA solar também gera danos no DNA, mas a genotoxicidade dessa radiação não explica inteiramente o seu impacto biológico. Atualmente, sabe-se que a radiação UVA é absorvida por cromóforos celulares, gerando espécies reativas de oxigênio, como o oxigênio singlete. Sabendo que o proteoma é um mediador de respostas ao estresse celular, nós investigamos os efeitos celulares de uma dose não-citotóxica de radiação UVA, equivalente a cerca de 20 minutos de exposição ao sol, no proteoma de queratinócitos humanos. Utilizando espectrometria de massas, bioinformática e ensaios bioquímicos convencionais, nós analisamos dois aspectos do estresse induzido por radiação UVA: o remodelamento espacial do proteoma 30 minutos depois do estresse e alterações nos níveis e na secreção de proteínas no longo prazo (24 horas e 7 dias depois da irradiação). Na primeira parte desta tese, nós quantificamos e atribuímos classificações de localização subcelular a mais de 3000 proteínas. Dentre essas proteínas, 600 tem potencialmente a sua distribuição subcelular alterada em resposta à radiação. As redistribuições subcelulares são acompanhadas de modulações redox, fragmentação mitocondrial e danos no DNA. Na segunda parte da tese, os nossos resultados mostraram que queratinócitos humanos primários entram em senescência sob exposição a uma única dose de radiação UVA, montando respostas antioxidantes e pró-inflamatórias. Células sob senescência induzida por UVA, por sua vez, desencadeiam respostas parácrinas em queratinócitos pré-tumorais (células HaCaT) por meio de mediadores inflamatórios. Em conjunto, esses resultados reiteram o papel da radiação UVA como um potente estressor metabólico em células da pele

Self-Organizing Maps for Cellular In Silico Staining and Cell Substate Classification.

Cellular composition and structural organization of cells in the tissue determine effective antitumor response and can predict patient outcome and therapy response. Here we present Seg-SOM, a method for dimensionality reduction of cell morphology in H&E-stained tissue images. Seg-SOM resolves cellular tissue heterogeneity and reveals complex tissue architecture. We leverage a self-organizing map (SOM) artificial neural network to group cells based on morphological features like shape and size. Seg-SOM allows for cell segmentation, systematic classification, and in silico cell labeling. We apply the Seg-SOM to a dataset of breast cancer progression images and find that clustering of SOM classes reveals groups of cells corresponding to fibroblasts, epithelial cells, and lymphocytes. We show that labeling the Lymphocyte SOM class on the breast tissue images accurately estimates lymphocytic infiltration. We further demonstrate how to use Seq-SOM in combination with non-negative matrix factorization to statistically describe the interaction of cell subtypes and use the interaction information as highly interpretable features for a histological classifier. Our work provides a framework for use of SOM in human pathology to resolve cellular composition of complex human tissues. We provide a python implementation and an easy-to-use docker deployment, enabling researchers to effortlessly featurize digitalized H&E-stained tissue.

Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient.

Pathological examination is the gold standard for cancer diagnosis, and breast tumor cells are often found in clusters. We report a case study on one triple-negative breast cancer (TNBC) patient, analyzing tumor development, metastasis, and prognosis with simultaneous DNA and RNA sequencing of pathologist-defined cell clusters from multiregional frozen sections. The cell clusters are isolated by laser capture microdissection (LCM) from primary tumor tissue, lymphatic vessels, and axillary lymph nodes. Data are reported for a total of 97 cell clusters. A combination of tumor cell-cluster clonality and phylogeny reveals 3 evolutionarily distinct pathways for this patient, each associated with a unique mRNA signature, and each correlated with disparate survival outcomes. Hub gene analysis indicates that extensive downregulation of ribosomal protein mRNA is a potential marker of poor prognosis in breast cancer.

Regulation of thymic T regulatory cell differentiation by TECs in health and disease.

The thymus produces self-limiting and self-tolerant T cells through the interaction between thymocytes and thymus epithelial cells (TECs), thereby generating central immune tolerance. The TECs are composed of cortical and medullary thymic epithelial cells, which regulate the positive and negative selection of T cells, respectively. During the process of negative selection, thymocytes with self-reactive ability are deleted or differentiated into regulatory T cells (Tregs). Tregs are a subset of suppressor T cells that are important for maintaining immune homeostasis. The differentiation and development of Tregs depend on the development of TECs and other underlying molecular mechanisms. Tregs regulated by thymic epithelial cells are closely related to human health and are significant in autoimmune diseases, thymoma and pregnancy. In this review, we summarize the current molecular and transcriptional regulatory mechanisms by which TECs affect the development and function of thymic Tregs. We also review the pathophysiological models of thymic epithelial cells regulating thymic Tregs in human diseases and specific physiological conditions.

Comparative Study of SARS-CoV-2, SARS-CoV-1, MERS-CoV, HCoV-229E and Influenza Host Gene Expression in Asthma: Importance of Sex, Disease Severity, and Epithelial Heterogeneity.

Epithelial characteristics underlying the differential susceptibility of chronic asthma to SARS-CoV-2 (COVID-19) and other viral infections are currently unclear. By revisiting transcriptomic data from patients with Th2 low versus Th2 high asthma, as well as mild, moderate, and severe asthmatics, we characterized the changes in expression of human coronavirus and influenza viral entry genes relative to sex, airway location, and disease endotype. We found sexual dimorphism in the expression of SARS-CoV-2-related genes ACE2, TMPRSS2, TMPRSS4, and SLC6A19. ACE2 receptor downregulation occurred specifically in females in Th2 high asthma, while proteases broadly assisting coronavirus and influenza viral entry, TMPRSS2, and TMPRSS4, were highly upregulated in both sexes. Overall, changes in SARS-CoV-2-related gene expression were specific to the Th2 high molecular endotype of asthma and different by asthma severity and airway location. The downregulation of ACE2 (COVID-19, SARS) and ANPEP (HCoV-229E) viral receptors wascorrelated with loss of club and ciliated cells in Th2 high asthma. Meanwhile, the increase in DPP4 (MERS-CoV), ST3GAL4, and ST6GAL1 (influenza) was associated with increased goblet and basal activated cells. Overall, this study elucidates sex, airway location, disease endotype, and changes in epithelial heterogeneity as potential factors underlying asthmatic susceptibility, or lack thereof, to SARS-CoV-2.

Airway basal stem cells generate distinct subpopulations of PNECs.

Pulmonary neuroendocrine cells (PNECs) have crucial roles in airway physiology and immunity by producing bioactive amines and neuropeptides (NPs). A variety of human diseases exhibit PNEC hyperplasia. Given accumulated evidence that PNECs represent a heterogenous population of cells, we investigate how PNECs differ, whether the heterogeneity is similarly present in mouse and human cells, and whether specific disease involves discrete PNECs. Herein, we identify three distinct types of PNECs in human and mouse airways based on single and double positivity for TUBB3 and the established NP markers. We show that the three PNEC types exhibit significant differences in NP expression, homeostatic turnover, and response to injury and disease. We provide evidence that these differences parallel their distinct cell of origin from basal stem cells (BSCs) or other airway epithelial progenitors.

A Classification Method for the Cellular Images Based on Active Learning and Cross-Modal Transfer Learning.

In computer-aided diagnosis (CAD) systems, the automatic classification of the different types of the human epithelial type 2 (HEp-2) cells represents one of the critical steps in the diagnosis procedure of autoimmune diseases. Most of the methods prefer to tackle this task using the supervised learning paradigm. However, the necessity of having thousands of manually annotated examples constitutes a serious concern for the state-of-the-art HEp-2 cells classification methods. We present in this work a method that uses active learning in order to minimize the necessity of annotating the majority of the examples in the dataset. For this purpose, we use cross-modal transfer learning coupled with parallel deep residual networks. First, the parallel networks, which take simultaneously different wavelet coefficients as inputs, are trained in a fully supervised way by using a very small and already annotated dataset. Then, the trained networks are utilized on the targeted dataset, which is quite larger compared to the first one, using active learning techniques in order to only select the images that really need to be annotated among all the examples. The obtained results show that active learning, when mixed with an efficient transfer learning technique, can allow one to achieve a quite pleasant discrimination performance with only a few annotated examples in hands. This will help in building CAD systems by simplifying the burdensome task of labeling images while maintaining a similar performance with the state-of-the-art methods.

A single-cell atlas of the healthy breast tissues reveals clinically relevant clusters of breast epithelial cells.

Single-cell RNA sequencing (scRNA-seq) is an evolving technology used to elucidate the cellular architecture of adult organs. Previous scRNA-seq on breast tissue utilized reduction mammoplasty samples, which are often histologically abnormal. We report a rapid tissue collection/processing protocol to perform scRNA-seq of breast biopsies of healthy women and identify 23 breast epithelial cell clusters. Putative cell-of-origin signatures derived from these clusters are applied to analyze transcriptomes of ~3,000 breast cancers. Gene signatures derived from mature luminal cell clusters are enriched in ~68% of breast cancers, whereas a signature from a luminal progenitor cluster is enriched in ~20% of breast cancers. Overexpression of luminal progenitor cluster-derived signatures in HER2+, but not in other subtypes, is associated with unfavorable outcome. We identify TBX3 and PDK4 as genes co-expressed with estrogen receptor (ER) in the normal breasts, and their expression analyses in >550 breast cancers enable prognostically relevant subclassification of ER+ breast cancers.

Regulation of immune responses by the airway epithelial cell landscape.

The community of cells lining our airways plays a collaborative role in the preservation of immune homeostasis in the lung and provides protection from the pathogens and pollutants in the air we breathe. In addition to its structural attributes that provide effective mucociliary clearance of the lower airspace, the airway epithelium is an immunologically active barrier surface that senses changes in the airway environment and interacts with resident and recruited immune cells. Single-cell RNA-sequencing is illuminating the cellular heterogeneity that exists in the airway wall and has identified novel cell populations with unique molecular signatures, trajectories of differentiation and diverse functions in health and disease. In this Review, we discuss how our view of the airway epithelial landscape has evolved with the advent of transcriptomic approaches to cellular phenotyping, with a focus on epithelial interactions with the local neuronal and immune systems.

Identificação de alterações bioquímicas em células epiteliais bronquiais humanas normais expostas a fumarato / Identification of biochemical changes in normal human bronchial epitelial cells exposed to fumarate

A reprogramação metabólica de células do câncer é apontada como uma característica essencial para o desenvolvimento da doença (cancer hallmark). Estudos mostram que mutações na enzima fumarato hidratase levam ao aumento da concentração intra e extracelular de fumarato, o que ocorre paralelamente à indução da transformação maligna. Neste trabalho, a fim de entender se o excesso de fumarato extracelular pode propiciar a transformação de células normais, foram quantificados alguns endpoints relacionados aos efeitos do fumarato e à transformação maligna, além de alterações metabólicas em células imortalizadas de epitélio brônquico humano normal (BEAS-2B) expostas ao fumarato. Uma vez que fumarato nas concentrações de 0,1 a 10 mM ao longo de 144 h não foi citotóxico, foram selecionadas as concentrações de 1 mM, 5 mM e 10 mM para as incubações. Fumarato induziu a formação de colônias em soft-agar após o período de sete dias (168 h) de exposição, o que indica a indução de transformação celular. Fumarato é um oncometabólito que inibe enzimas que dependem de α-cetoglutarato como co-substrato, dentre as quais as enzimas ten eleven translocation (TET) que catalisam a formação de 5-hidroximetilcitosina (5-hmC) a partir de 5-metilcitosina (5-mC), o primeiro passo da sequência de reações que levam à desmetilação do DNA. Os níveis totais de 5-hmC estavam diminuídos no DNA das células expostas. Colônias retiradas do soft-agar (controle, 1, 5 e 10 mM de fumarato) foram cultivadas e, após 90 dias em cultura, as células foram submetidas ao ensaio de invasão e migração em câmara de Boyden (transwell), tendo sido observada maior capacidade de migração/invasão das células anteriormente expostas ao fumarato. Foi observada indução de estresse redox nas células expostas ao fumarato. A partir da quantificação de metabólitos intracelulares por HPLC-ESI-MS/MS e HPLC-ESI-Q-TOF, verificamos que as células BEAS-2B absorveram o fumarato adicionado ao meio de cultura, o qual foi convertido intracelularmente a malato, aspartato, argininosuccinato, citrato, succinato e glutamato. O oncometabólito 2-L-hidroxiglutarato foi detectado em níveis aumentados nas células expostas a fumarato, assim como adenosina, enquanto que NAD+ e NADP+ apareceram diminuídos. As alterações metabólicas na presença de fumarato contribuíram para a manutenção do balanço energético das células, ou mesmo para um saldo positivo de energia. A exposição das células a [13C4]fumarato permitiu a análise do fluxo inicial do fumarato absorvido pelas células. A partir dessa análise verificamos que o fumarato absorvido entra no ciclo de Krebs, gerando malato, que é em grande parte desviado para reações externas ao ciclo, como a geração de aspartato e argininosuccinato. Citrato proveniente das reações de [13C4]fumarato no ciclo de Krebs foi detectado em níveis inferiores aos endógenos. O uso de [13C4]fumarato permitiu a visualização da geração de [13C4]succinato, que tem como possível fonte a atividade reversa da succinato desidrogenase. Verificamos também a geração de [13C3]glutamato. Supõe-se que as alterações metabólicas induzidas pelo fumarato absorvido pelas células BEAS-2B contribuam para a modulação da expressão de genes e da atividade de proteínas que favorecem o processo tumorigênico

The metabolic reprogramming of cancer cells is identified as an essential feature for the development of the disease (a cancer hallmark). Studies show that mutations in the enzyme fumarate hydratase lead to increased intra- and extracellular fumarate concentration, which occurs in parallel with the induction of malignant transformation. In this work, in order to understand if excess extracellular fumarate can lead to the transformation of normal cells, some endpoints related to the effects of fumarate and malignant transformation were quantified, as well as metabolic alterations in the immortalized normal human bronchial epithelial cell line BEAS-2B exposed to fumarate. Since fumarate at concentrations from 0.1 to 10 mM over 144 h was not cytotoxic, the concentrations of 1 mM, 5 mM and 10 mM were selected for incubations. Fumarate induced colony formation in soft agar after the seven day (168 h) exposure period, which indicates the induction of cell transformation. Fumarate is an oncometabolite that inhibits α-ketoglutarate-dependent enzymes, among which are ten eleven translocation (TET) enzymes that catalyze the formation of 5-hydroxymethylcytosine (5-hmC) from 5-methylcytosine (5-mC), the first step in the sequence of reactions leading to DNA demethylation. Total 5-hmC levels were decreased in the DNA of exposed cells. Colonies removed from the soft-agar (control, 1, 5 and 10 mM fumarate) were cultured and after 90 days in culture the cells were subjected to the Boyden chamber (transwell) invasion and migration assay, and a greater capacity for migration/invasion of cells previously exposed to fumarate was observed. Redox stress induction was observed in cells exposed to fumarate. From the quantification of intracellular metabolites by HPLC-ESI-MS/MS and HPLC-ESI-Q-TOF, we found that BEAS-2B cells absorbed the fumarate added to the culture medium, which was intracellularly converted to malate, aspartate, argininosuccinate, citrate, succinate and glutamate. The oncometabolite 2-L-hydroxyglutarate was detected at increased levels in cells exposed to fumarate, as well as adenosine, while NAD+ and NADP+ appeared decreased. Metabolic changes in the presence of fumarate contributed to the maintenance of the energy balance of the cells, or even to a positive energy balance. Exposure of cells to [13C4]fumarate allowed the analysis of the initial flow of the fumarate absorbed by the cells. From this analysis we found that the absorbed fumarate entered the Krebs cycle, generating malate, which was largely diverted to reactions outside the cycle, such as the generation of aspartate and argininosuccinate. Citrate from the reactions of [13C4]fumarate in the Krebs cycle was detected at levels lower than endogenous. The use of [13C4]fumarate allowed the detection of [13C4]succinate, which has as its possible source the reverse activity of succinate dehydrogenase. We also observed the generation of [13C3]glutamate. The metabolic changes induced by the absorbed fumarate are supposed to contribute to the modulation of gene expression and protein activity that favor the tumorigenic process

Modulação da concentração intracelular de NAD+ e seu efeito na tumorigênese induzida por benzo[a]pireno em células bronquiais epiteliais humanas / Modulation of intracellular concentration of NAD+ and its effect on benzo[a]pyrene-induced tumorigenesis in human epithelial bronchial cells

A alta incidência, prevalência e mortalidade do câncer de pulmão demonstram a necessidade de se identificar alterações moleculares envolvidas na carcinogênese pulmonar. Nesse contexto, a reprogramação do metabolismo energético é uma marca emergente do câncer. Há evidências de que benzo[a]pireno (B[a]P), um conhecido carcinógeno humano, induz alterações metabólicas via modificação da função mitocondrial tanto in vitro quanto in vivo. Uma vez que as alterações metabólicas não são somente o resultado da transformação celular, mas podem também ter papel na etiologia do câncer ao modular o epigenoma e a expressão de genes, intervir no metabolismo de células em processo de transformação pode contribuir para desvendar mecanismos de carcinogênese e revelar alvos para quimioprevenção. A fim de investigar a relação entre alterações no metabolismo celular, marcas epigenéticas e transformação celular, implementamos um modelo de tumorigênese (avaliada pela formação de colônias em soft-agar) induzida por B[a]P em células epiteliais bronquiais humanas imortalizadas (linhagem BEAS-2B) crescidas em monocamada (2D). O modelo possibilitou a observação de alterações precoces do metabolismo celular. Levando em consideração que o nucleotídeo NAD+ regula as atividades de diversas vias moleculares importantes para a sobrevivência, diferenciação, crescimento e morte celular, e que suas concentrações foram rapidamente diminuídas após exposição a B[a]P, decidimos suplementar as células BEAS-2B com nicotinamida ribosídeo (NR), um precursor intracelular de NAD+, concomitantemente à exposição a B[a]P. NR em baixa concentração no meio de cultura (1 µM) induziu estresse energético em células BEAS-2B expostas a B[a]P (1 µM) ao longo do período de uma semana de co-incubação, aumentando seletivamente a taxa de apoptose dessas células. Protegeu contra a transformação celular induzida por B[a]P e impediu completamente a formação espontânea de colônias das células controle em soft-agar. Usamos uma abordagem metabolômica direcionada a alvos específicos ("targeted metabolomics") desenvolvida no grupo para quantificar metabólitos conhecidamente alterados no câncer. Os dados indicam que NR diminui o metabolismo de glutamina nas células expostas a B[a]P, o que ocorre em paralelo com a diminuição das concentrações de citrato e aspartato, aumento da razão malato/aspartato, diminuição das razões ATP/AMP e ATP/ADP e aumento das concentrações de adenosina. As alterações se enquadram na hipótese de inibição do shuttle malato-aspartato, cuja atividade é necessária para a sobrevivência de células que sofrem o efeito Warburg (alta dependência de NADH citosólico para geração de ATP). NR adicionalmente protegeu as células contra o estresse redox, a hipermetilação do DNA e o aumento da atividade de sirtuína 1 (SIRT1) induzidos por B[a]P, além de aumentar a expressão de genes supressores tumorais (E-caderina, PTEN, semaforina 3F, p16(ink4a)) que podem ser reprimidos por CtBP (proteína ligante de NADH que atua como sensor redox e traduz a condição metabólica da célula para o controle da expressão gênica). Foi ainda observada maior atividade de PARP1 nas células expostas a B[a]P+NR em comparação aos demais grupos. Os resultados obtidos mostram que NR se contrapõe a ou exacerba alterações bioquímicas induzidas por B[a]P, diminuindo a chance de transformação carcinogênica das células BEAS-2B. Estudos em modelos mais complexos, como micro tecidos in vitro, são necessários para a confirmação do efeito quimiopreventivo da NR e alterações bioquímicas subjacentes

Tese de DoutoradoDOIhttps://doi.org/10.11606/T.9.2021.tde-05082021-095853DocumentoTese de DoutoradoAutorCordeiro, Everson Willian Fialho (Catálogo USP)Nome completoEverson Willian Fialho CordeiroE-mailE-mailUnidade da USPFaculdade de Ciências FarmacêuticasÁrea do ConhecimentoToxicologiaData de Defesa2021-04-08ImprentaSão Paulo, 2021OrientadorLoureiro, Ana Paula de Melo (Catálogo USP) Banca examinadoraLoureiro, Ana Paula de Melo (Presidente) Àvila, Daiana Silva de Meotti, Flavia Carla Silva, Eloiza Helena Tajara da Título em portuguêsModulação da concentração intracelular de NAD+ e seu efeito na tumorigênese induzida por benzo[a]pireno em células bronquiais epiteliais humanasPalavras-chave em portuguêsBenzo[a]pireno Câncer de pulmão Metabolismo energético Nicotinamida ribosídeo Resumo em portuguêsA alta incidência, prevalência e mortalidade do câncer de pulmão demonstram a necessidade de se identificar alterações moleculares envolvidas na carcinogênese pulmonar. Nesse contexto, a reprogramação do metabolismo energético é uma marca emergente do câncer. Há evidências de que benzo[a]pireno (B[a]P), um conhecido carcinógeno humano, induz alterações metabólicas via modificação da função mitocondrial tanto in vitro quanto in vivo. Uma vez que as alterações metabólicas não são somente o resultado da transformação celular, mas podem também ter papel na etiologia do câncer ao modular o epigenoma e a expressão de genes, intervir no metabolismo de células em processo de transformação pode contribuir para desvendar mecanismos de carcinogênese e revelar alvos para quimioprevenção. A fim de investigar a relação entre alterações no metabolismo celular, marcas epigenéticas e transformação celular, implementamos um modelo de tumorigênese (avaliada pela formação de colônias em soft-agar) induzida por B[a]P em células epiteliais bronquiais humanas imortalizadas (linhagem BEAS-2B) crescidas em monocamada (2D). O modelo possibilitou a observação de alterações precoces do metabolismo celular. Levando em consideração que o nucleotídeo NAD+ regula as atividades de diversas vias moleculares importantes para a sobrevivência, diferenciação, crescimento e morte celular, e que suas concentrações foram rapidamente diminuídas após exposição a B[a]P, decidimos suplementar as células BEAS-2B com nicotinamida ribosídeo (NR), um precursor intracelular de NAD+, concomitantemente à exposição a B[a]P. NR em baixa concentração no meio de cultura (1 µM) induziu estresse energético em células BEAS-2B expostas a B[a]P (1 µM) ao longo do período de uma semana de co-incubação, aumentando seletivamente a taxa de apoptose dessas células. Protegeu contra a transformação celular induzida por B[a]P e impediu completamente a formação espontânea de colônias das células controle em soft-agar. Usamos uma abordagem metabolômica direcionada a alvos específicos ("targeted metabolomics") desenvolvida no grupo para quantificar metabólitos conhecidamente alterados no câncer. Os dados indicam que NR diminui o metabolismo de glutamina nas células expostas a B[a]P, o que ocorre em paralelo com a diminuição das concentrações de citrato e aspartato, aumento da razão malato/aspartato, diminuição das razões ATP/AMP e ATP/ADP e aumento das concentrações de adenosina. As alterações se enquadram na hipótese de inibição do shuttle malato-aspartato, cuja atividade é necessária para a sobrevivência de células que sofrem o efeito Warburg (alta dependência de NADH citosólico para geração de ATP). NR adicionalmente protegeu as células contra o estresse redox, a hipermetilação do DNA e o aumento da atividade de sirtuína 1 (SIRT1) induzidos por B[a]P, além de aumentar a expressão de genes supressores tumorais (E-caderina, PTEN, semaforina 3F, p16(ink4a)) que podem ser reprimidos por CtBP (proteína ligante de NADH que atua como sensor redox e traduz a condição metabólica da célula para o controle da expressão gênica). Foi ainda observada maior atividade de PARP1 nas células expostas a B[a]P+NR em comparação aos demais grupos. Os resultados obtidos mostram que NR se contrapõe a ou exacerba alterações bioquímicas induzidas por B[a]P, diminuindo a chance de transformação carcinogênica das células BEAS-2B. Estudos em modelos mais complexos, como micro tecidos in vitro, são necessários para a confirmação do efeito quimiopreventivo da NR e alterações bioquímicas subjacentes.Título em inglêsModulation of intracellular concentration of NAD+ and its effect on benzo[a]pyrene-induced tumorigenesis in human epithelial bronchial cellsPalavras-chave em inglêsBenzo[a]pyrene Energetic metabolism Lung cancer Nicotinamide riboside Resumo em inglêsThe high incidence, prevalence and mortality of lung cancer demonstrates the need to identify molecular changes involved in lung carcinogenesis. In this context, the reprogramming of energy metabolism is an emerging brand of cancer. There is evidence that benzo[a]pyrene (B[a]P), a known human carcinogen, induces metabolic changes via modification of mitochondrial function both in vitro and in vivo. Since metabolic changes are not only the result of cell transformation, but can also play a role in the etiology of cancer by modulating the epigenome and gene expression, intervening in the metabolism of cells in the process of transformation can contribute to unravel mechanisms of carcinogenesis and reveal targets for chemoprevention. In order to investigate the relationship between changes in cell metabolism, epigenetic marks and cell transformation, we implemented a model of tumorigenesis (assessed by the formation of colonies on soft-agar) induced by B[a]P in immortalized human bronchial epithelial cells (BEAS-2B cell line human) grown in monolayer (2D). The model enabled the observation of early changes in cell metabolism. Taking into account that the NAD+ nucleotide regulates the activities of several molecular pathways important for cell survival, differentiation, growth and death, and that their concentrations were rapidly decreased after exposure to B[a]P, we decided to supplement the BEAS-2B cells with nicotinamide riboside (NR), an intracellular precursor of NAD+, concomitantly with exposure to B[a]P. NR in low concentration in the culture medium (1 µM) induced energy stress in BEAS-2B cells exposed to B[a]P (1 µM) over the period of a week of co-incubation, selectively increasing the apoptosis rate of these cells. It protected against cell transformation induced by B[a]P and completely prevented the spontaneous formation of control cell colonies on soft-agar. We use a targeted metabolomics approach developed in the group to quantify metabolites known to be altered in cancer. The data indicate that NR decreases the glutamine metabolism in cells exposed to B[a]P, which occurs in parallel with the decrease in citrate and aspartate concentrations, increased malate/aspartate ratio, decreased ATP/AMP and ATP/ADP ratios and increased adenosine concentrations. The changes fit the hypothesis of inhibition of the malate-aspartate shuttle, whose activity is necessary for the survival of cells that suffer the Warburg effect (high dependence on cytosolic NADH for ATP generation). NR additionally protected cells against redox stress, DNA hypermethylation and increased B[a]P-induced sirtuin 1 (SIRT1) activity, in addition to increasing the expression of tumor suppressor genes (E-cadherin, PTEN, semaphorin 3F, p16 (ink4a)) that can be suppressed by CtBP (NADH-binding protein that acts as a redox sensor and translates the cell's metabolic condition to control gene expression). Higher PARP1 activity was also observed in cells exposed to B[a]P+NR compared to the other groups. The results obtained show that NR is opposed to or exacerbates biochemical changes induced by B[a]P, reducing the chance of carcinogenic transformation of BEAS-2B cells. Studies on more complex models, such as micro tissues in vitro, are necessary to confirm the chemopreventive effect of NR and underlying biochemical changes

Regorafenib Suppresses Migration of and Induces Cell Cycle Arrest and Apoptosis in MCF-7 Cells

This study investigated the mechanism underlying the suppression of estrogen receptor-positive MCF-7 cell growth by regorafenib. MCF-7 cells were treated with regorafenib, and the effect of regorafenib on multiple cancer-associated pathways was evaluated. Although regorafenib effectively inhibited the proliferation of MCF-7 cells, it had no effect on the proliferation of the normal breast epithelial cell line MCF10A. Regorafenib suppressed MCF-7 cell migration, probably by regulating the homeostatic expression of matrix metalloproteinases and the tissue inhibitor of MMPs. Furthermore, it upregulated p21 expression, downregulated cyclin B1 and cyclin D1 expresssions, and caused cell cycle arrest. In addition, regorafenib induced apoptosis in MCF-7 cells by reducing Mcl-1 expression and activating caspase signaling. These results demonstrate that regorafenib has the potential to be an effective drug for treating breast cancer

Different iron-handling in inflamed small and large cholangiocytes and in small and large-duct type intrahepatic cholangiocarcinoma.

Cholangiocarcinoma (CCA) represents the second most common primary hepatic malignancy and originates from the neoplastic transformation of the biliary cells. The intrahepatic subtype includes two morpho-molecular forms: large-duct type intrahepatic CCA (iCCA) and small-duct type iCCA. Iron is fundamental for the cellular processes, contributing in tumor development and progression. The aim of this study was to evaluate iron uptake, storage, and efflux proteins in both lipopolysaccharide-inflamed small and large cholangiocytes as well as in different iCCA subtypes. Our results show that, despite an increase in interleukin-6 production by both small and large cholangiocytes, ferroportin (Fpn) was decreased only in small cholangiocytes, whereas transferrin receptor-1 (TfR1) and ferritin (Ftn) did not show any change. Differently from in vitro models, Fpn expression was increased in malignant cholangiocytes of small-duct type iCCA in comparison to large-duct type iCCA and peritumoral tissues. TfR1, Ftn and hepcidin were enhanced, even if at different extent, in both malignant cholangiocytes in comparison to the surrounding samples. Lactoferrin was higher in large-duct type iCCA in respect to small-duct type iCCA and peritumoral tissues. These findings show a different iron handling by inflamed small and large cholangiocytes, and small and large-duct type iCCA. The difference in iron homeostasis by the iCCA subtypes may have implications for the tumor management.

Cells of the adult human heart.

Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors.

Understanding the cellular constituents of the prostate is essential for identifying the cell of origin for prostate adenocarcinoma. Here, we describe a comprehensive single-cell atlas of the adult mouse prostate epithelium, which displays extensive heterogeneity. We observe distal lobe-specific luminal epithelial populations (LumA, LumD, LumL, and LumV), a proximally enriched luminal population (LumP) that is not lobe-specific, and a periurethral population (PrU) that shares both basal and luminal features. Functional analyses suggest that LumP and PrU cells have multipotent progenitor activity in organoid formation and tissue reconstitution assays. Furthermore, we show that mouse distal and proximal luminal cells are most similar to human acinar and ductal populations, that a PrU-like population is conserved between species, and that the mouse lateral prostate is most similar to the human peripheral zone. Our findings elucidate new prostate epithelial progenitors, and help resolve long-standing questions about anatomical relationships between the mouse and human prostate.

Automated classification of cells into multiple classes in epithelial tissue of oral squamous cell carcinoma using transfer learning and convolutional neural network.

The analysis of tissue of a tumor in the oral cavity is essential for the pathologist to ascertain its grading. Recent studies using biopsy images reveal computer-aided diagnosis for oral sub-mucous fibrosis (OSF) carried out using machine learning algorithms, but no research has yet been outlined for multi-class grading of oral squamous cell carcinoma (OSCC). Pertinently, with the advent of deep learning in digital imaging and computational aid in the diagnosis, multi-class classification of OSCC biopsy images can help in timely and effective prognosis and multi-modal treatment protocols for oral cancer patients, thus reducing the operational workload of pathologists while enhancing management of the disease. With this motivation, this study attempts to classify OSCC into its four classes as per the Broder's system of histological grading. The study is conducted on oral biopsy images applying two methods: (i) through the application of transfer learning using pre-trained deep convolutional neural network (CNN) wherein four candidate pre-trained models, namely Alexnet, VGG-16, VGG-19 and Resnet-50, were chosen to find the most suitable model for our classification problem, and (ii) by a proposed CNN model. Although the highest classification accuracy of 92.15% is achieved by Resnet-50 model, the experimental findings highlight that the proposed CNN model outperformed the transfer learning approaches displaying accuracy of 97.5%. It can be concluded that the proposed CNN based multi-class grading method of OSCC could be used for diagnosis of patients with OSCC.