Multiple Cellular Origins Research Articles

Tracing the origin of alveolar stem cells in lung repair and regeneration

Alveolar type 2 (AT2) cells are stem cells of the alveolar epithelia. Previous genetic lineage tracing studies reported multiple cellular origins for AT2 cells after injury. However, conventional lineage tracing based on Cre-loxP has the limitation of non-specific labeling. Here, we introduced a dual recombinase-mediated intersectional genetic lineage tracing approach, enabling precise investigation of AT2 cellular origins during lung homeostasis, injury, and repair. We found AT1 cells, being terminally differentiated, did not contribute to AT2 cells after lung injury and repair. Distinctive yet simultaneous labeling of club cells, bronchioalveolar stem cells (BASCs), and existing AT2 cells revealed the exact contribution of each to AT2 cells post-injury. Mechanistically, Notch signaling inhibition promotes BASCs but impairs club cells' ability to generate AT2 cells during lung repair. This intersectional genetic lineage tracing strategy with enhanced precision allowed us to elucidate the physiological role of various epithelial cell types in alveolar regeneration following injury.

Homemade: building the structure of the neurogenic niche.

Neural stem/progenitor cells live in an intricate cellular environment, the neurogenic niche, which supports their function and enables neurogenesis. The niche is made of a diversity of cell types, including neurons, glia and the vasculature, which are able to signal to and are structurally organised around neural stem/progenitor cells. While the focus has been on how individual cell types signal to and influence the behaviour of neural stem/progenitor cells, very little is actually known on how the niche is assembled during development from multiple cellular origins, and on the role of the resulting topology on these cells. This review proposes to draw a state-of-the art picture of this emerging field of research, with the aim to expose our knowledge on niche architecture and formation from different animal models (mouse, zebrafish and fruit fly). We will span its multiple aspects, from the existence and importance of local, adhesive interactions to the potential emergence of larger-scale topological properties through the careful assembly of diverse cellular and acellular components.

Generation of specialized blood vessels via lymphatic transdifferentiation.

The lineage and developmental trajectory of a cell are key determinants of cellular identity. In the vascular system, endothelial cells (ECs) of blood and lymphatic vessels differentiate and specialize to cater to the unique physiological demands of each organ1,2. Although lymphatic vessels were shown to derive from multiple cellular origins, lymphatic ECs (LECs) are not known to generate other cell types3,4. Here we use recurrent imaging and lineage-tracing of ECs in zebrafish anal fins, from early development to adulthood, to uncover a mechanism of specialized blood vessel formation through the transdifferentiation of LECs. Moreover, we demonstrate that deriving anal-fin vessels from lymphatic versus blood ECs results in functional differences in the adult organism, uncovering a link between cell ontogeny and functionality. Wefurther use single-cell RNA-sequencing analysis to characterize the different cellular populations and transition states involved in the transdifferentiation process. Finally, we show that, similar to normal development, the vasculature is rederived from lymphatics during anal-fin regeneration, demonstratingthat LECs in adult fish retain both potency and plasticity for generating blood ECs. Overall, our research highlights an innate mechanism of blood vessel formation through LEC transdifferentiation, and provides in vivo evidence for a link between cell ontogeny and functionality in ECs.

Pineal parenchymal tumour of intermediate differentiation: A case report

Pineal parenchymal tumours (PPTs) represent one third of the pineal region tumours. PPTs are subdivided into pineocytoma (PC), pineoblastoma (PB) and PPT with intermediate differentiation (PPTID). We report radiological, morphological and immunochemical features which permit to grade these tumours. Tumors of the pineal region can arise from multiple cellular origins and thus represent a very heterogeneous group of pathologies.Within the subgroup of pineal parenchymal tumors, there is a histopathologic spectrum ranging from pineocytoma to pineal parenchymal tumors of intermediate differentiation to pineoblastoma. The currentWorld Health Organization classification and the histopathologic features of the pineal parenchymal tumor subtypes with intermediate differentiation are described. Keywords: Pineal parenchymal tumours, Pineal parenchymal tumours with, Intermediate differentiation, Pineoblastoma and Pineocytoma.

Key Developmental Regulators Suggest Multiple Origins of Pancreatic Beta Cell Regeneration.

Extensive efforts have been done to try to restore the lost β cell mass for the cure of diabetes. Animal models have been established to provide evidences of cellular origins and contextual regulators of β cell regeneration. Here, we used a zebrafish β cell ablation and regeneration model to investigate β cell neogenesis in the first few days after a near-total β cell loss. Regeneration of β cells first occurred within 7 h post-treatment. Developmental regulators such as neurod, pdx1, mnx1, and nkx2.2a were active in the regenerating β cells, while at the same time suggesting different subpopulations of regenerative cellular origins. Using Cre/loxP-based lineage tracing, we showed that intrapancreatic ductal cells resisted to give rise to regenerating β cells. Given that transdifferentiation of α cell and δ cell can regenerate β cell, here we have provided further molecular evidence highly suggesting that the regenerating β cells originate from multiple cellular origins.

Cholangiocarcinoma: Classification, Histopathology and Molecular Carcinogenesis.

Cholangiocarcinoma (CC) is the second most common tumor of the liver, originating from the biliary system with increasing incidence and mortality worldwide. Several new classifications review the significance of tumor localization, site of origin, proliferation and biomarkers in the intrahepatic, perihilar and distal forms of the lesion. Based on growth pattern mass-forming, periductal-infiltrating, intraductal, undefined and mixed types are differentiated. There are further subclassifications which are applied for the histological features, in particular for intrahepatic CC. Recognition of the precursors and early lesions of CC including biliary intraepithelial neoplasia (BilIN), intraductal papillary neoplasm of the bile ducts (IPNB), biliary mucinous cystic neoplasm (MCNB) and the candidate precursors, such as bile duct adenoma and von Meyenburg complex is of increasing significance. In addition to the previously used biliary markers detected by immunohistochemistry, several new markers have been added to the differentiation of both the benign and malignant lesions, which can be used to aid in the subclassification in association with the outcome of CC. Major aspects of biliary carcinogenesis have been revealed, yet, the exact way of this diverse process is still unclear. The factors contributing to molecular cholangiocarcinogenesis include various risk factors, different anatomical localizations, multiple cellular origins, genetic and epigenetic alterations, tumor microenvironment, heterogeneity and clonal evolution. Driver mutations have been identified, implying that they are optimal candidates for targeted therapy. The most promising therapeutic candidates have entered clinical trials.

Numerous Ontogenetic Roads to Mantle Cell Lymphoma: Immunogenetic and Immunohistochemical Evidence

To obtain insight into the ontogeny of mantle cell lymphoma (MCL), we assessed 206 patients from a morphological, immunohistochemical, and immunogenetic perspective. Our series included nodal (n=151), extranodal (n=28), and primary splenic (n=27) MCL cases. Skewing of the immunoglobulin heavy variable (IGHV) gene repertoire was noted, with only four IGHV genes accounting for 46% of cases and approximately 70% of cases (107/154) bearing an imprint of somatic hypermutation (SHM) ranging from minimal to pronounced. Interestingly, a distinctive immunophenotypic and immunogenetic profile was identified for primary splenic MCL, which was enriched for DBA.44-positive cases (P<0.001) and used the IGHV1-8 gene more frequently (P=0.02) compared to nodal or extranodal cases, alluding to distinct immunopathogenetic and antigen selection processes. Expression of CD27 (considered a marker of activated B cells) was generally dissociated from SHM and was more prevalent in cases with no or minimal/borderline SHM. These findings support the idea that antigen drive is relevant for most MCL cases, although the specific antigens and the precise location of affinity maturation remain to be elucidated. Moreover, they raise the intriguing hypothesis of multiple cellular origins for MCL.

Multidimensional Analysis of Protease Substrates and Their Cellular Origins in Mixed Secretomes from Multiple Cell Types.

Although extracellular proteases are confronted with substrate proteins expressed by multiple cell types in vivo, in most protease substrate discovery approaches, the test protease is exposed to a test proteome (secretome) derived only from a single cell type. This limits the potential substrate space and prohibits the formation of protein complexes constituted of components derived from multiple cellular origins. Mixing of secretomes collected from multiple cell types addresses this issue, but information on the cellular origin of a substrate protein is lost. Here, we describe a protocol and the corresponding data analysis workflow for a multidimensional substrate discovery approach termed SILAC -iTRAQ -TAILS that is based on hyperplexed terminal amine isotopic labeling of substrates (TAILS ), allowing identification of substrates and concomitant assignment to cellular origins in mixed secretomes within the same experiment.

Identification of Histological Correlates of Overall Survival in Lower Grade Gliomas Using a Bag-of-words Paradigm: A Preliminary Analysis Based on Hematoxylin & Eosin Stained Slides from the Lower Grade Glioma Cohort of The Cancer Genome Atlas

Background: Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO), which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs) (WHO Grade II–III) have fewer malignant characteristics than high-grade gliomas (WHO Grade IV), and a better clinical prognosis, however, accurate discrimination of overall survival (OS) remains a challenge. In this study, we aimed to identify tissue-derived image features using a machine learning approach to predict OS in a mixed histology and grade cohort of lower grade glioma patients. To achieve this aim, we used H and E stained slides from the public LGG cohort of The Cancer Genome Atlas (TCGA) to create a machine learned dictionary of “image-derived visual words” associated with OS. We then evaluated the combined efficacy of using these visual words in predicting short versus long OS by training a generalized machine learning model. Finally, we mapped these predictive visual words back to molecular signaling cascades to infer potential drivers of the machine learned survival-associated phenotypes. Methods: We analyzed digitized histological sections downloaded from the LGG cohort of TCGA using a bag-of-words approach. This method identified a diverse set of histological patterns that were further correlated with OS, histology, and molecular signaling activity using Cox regression, analysis of variance, and Spearman correlation, respectively. A support vector machine (SVM) model was constructed to discriminate patients into short and long OS groups dichotomized at 24-month. Results: This method identified disease-relevant phenotypes associated with OS, some of which are correlated with disease-associated molecular pathways. From these image-derived phenotypes, a generalized SVM model which could discriminate 24-month OS (area under the curve, 0.76) was obtained. Conclusion: Here, we demonstrated one potential strategy to incorporate image features derived from H and E stained slides into predictive models of OS. In addition, we showed how these image-derived phenotypic characteristics correlate with molecular signaling activity underlying the etiology or behavior of LGG.

Redefining the origin and evolution of ovarian cancer: a hormonal connection.

Ovarian cancer has the highest mortality of all female reproductive cancers. Late diagnosis, tumour heterogeneity and the development of chemoresistance contribute to this statistic and work against patient survival. Current studies have revealed novel concepts that impact our view on how ovarian cancer develops. The greatest impact is on our understanding that, as a disease, ovarian cancer has multiple cellular origins and that these malignant precursors are mostly derived from outside of the ovaries. In this review, we propose a new concept of a step-wise developmental process that may underwrite ovarian tumorigenesis and progression: (1) migration/recruitment to the ovaries; (2) seeding and establishment in the ovaries; (3) induction of a dormant cancer stage; and (4) expansion and tumor progression. We will discuss the relationship of each step with the changing ovarian function and milieu during the reproductive age and the subsequent occurrence of menopause. The realization that ovarian cancer development and progression occurs in distinct steps is critical for the search of adequate markers for early detection that will offer personalized strategies for prevention and therapy.

Multiple cellular origins and molecular evolution of intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignancy associated with unfavorable prognosis and for which no effective treatments are available. Its molecular pathogenesis is poorly understood. Genome-wide sequencing and high-throughput technologies have provided critical insights into the molecular basis of ICC while sparking a heated debate on the cellular origin. Cancer exhibits variabilities in origin, progression and cell biology. Recent evidence suggests that ICC has multiple cellular origins, including differentiated hepatocytes; intrahepatic biliary epithelial cells (IBECs)/cholangiocytes; pluripotent stem cells, such as hepatic stem/progenitor cells (HPCs) and biliary tree stem/progenitor cells (BTSCs); and peribiliary gland (PBG). However, both somatic mutagenesis and epigenomic features are highly cell type-specific. Multiple cellular origins may have profoundly different genomic landscapes and key signaling pathways, driving phenotypic variation and thereby posing significant challenges to personalized medicine in terms of achieving the optimal drug response and patient outcome. Considering this information, we have summarized the latest experimental evidence and relevant literature to provide an up-to-date view of the cellular origin of ICC, which will contribute to establishment of a hierarchical model of carcinogenesis and allow for improvement of the anatomical-based classification of ICC. These new insights have important implications for both the diagnosis and treatment of ICC patients.

Embryonic Development of the Bicuspid Aortic Valve

Bicuspid aortic valve (BAV) is the most common congenital valvular heart defect with an overall frequency of 0.5%–1.2%. BAVs result from abnormal aortic cusp formation during valvulogenesis, whereby adjacent cusps fuse into a single large cusp resulting in two, instead of the normal three, aortic cusps. Individuals with BAV are at increased risk for ascending aortic disease, aortic stenosis and coarctation of the aorta. The frequent occurrence of BAV and its anatomically discrete but frequent co-existing diseases leads us to suspect a common cellular origin. Although autosomal-dominant transmission of BAV has been observed in a few pedigrees, notably involving the gene NOTCH1, no single-gene model clearly explains BAV inheritance, implying a complex genetic model involving interacting genes. Several sequencing studies in patients with BAV have identified rare and uncommon mutations in genes of cardiac embryogenesis. But the extensive cell-cell signaling and multiple cellular origins involved in cardiac embryogenesis preclude simplistic explanations of this disease. In this review, we examine the series of events from cellular and transcriptional embryogenesis of the heart, to development of the aortic valve.

FOXF1 transcription factor is required for formation of embryonic vasculature by regulating VEGF signaling in endothelial cells.

Inactivating mutations in the Forkhead Box transcription factor F1 (FOXF1) gene locus are frequently found in patients with alveolar capillary dysplasia with misalignment of pulmonary veins, a lethal congenital disorder, which is characterized by severe abnormalities in the respiratory, cardiovascular, and gastrointestinal systems. In mice, haploinsufficiency of the Foxf1 gene causes alveolar capillary dysplasia and developmental defects in lung, intestinal, and gall bladder morphogenesis. Although FOXF1 is expressed in multiple mesenchyme-derived cell types, cellular origins and molecular mechanisms of developmental abnormalities in FOXF1-deficient mice and patients with alveolar capillary dysplasia with misalignment of pulmonary veins remain uncharacterized because of lack of mouse models with cell-restricted inactivation of the Foxf1 gene. In the present study, the role of FOXF1 in endothelial cells was examined using a conditional knockout approach. A novel mouse line harboring Foxf1-floxed alleles was generated by homologous recombination. Tie2-Cre and Pdgfb-CreER transgenes were used to delete Foxf1 from endothelial cells. FOXF1-deficient embryos exhibited embryonic lethality, growth retardation, polyhydramnios, cardiac ventricular hypoplasia, and vascular abnormalities in the lung, placenta, yolk sac, and retina. Deletion of FOXF1 from endothelial cells reduced endothelial proliferation, increased apoptosis, inhibited vascular endothelial growth factor signaling, and decreased expression of endothelial genes critical for vascular development, including vascular endothelial growth factor receptors Flt1 and Flk1, Pdgfb, Pecam1, CD34, integrin β3, ephrin B2, Tie2, and the noncoding RNA Fendrr. Chromatin immunoprecipitation assay demonstrated that Flt1, Flk1, Pdgfb, Pecam1, and Tie2 genes are direct transcriptional targets of FOXF1. FOXF1 is required for the formation of embryonic vasculature by regulating endothelial genes critical for vascular development and vascular endothelial growth factor signaling.

Fundamental diversity of human CpG islands at multiple biological levels

CpG islands (CGIs) are commonly used as genomic markers to study the patterns and regulatory consequences of DNA methylation. Interestingly, recent studies reveal a substantial diversity among CGIs: long and short CGIs, for example, exhibit contrasting patterns of gene expression complexity and nucleosome occupancy. Evolutionary origins of CGIs are also highly heterogeneous. In order to systematically evaluate potential diversities among CGIs and ultimately to illuminate the link between diversity of CGIs and their epigenetic variation, we analyzed the nucleotide-resolution DNA methylation maps (methylomes) of multiple cellular origins. We discover novel ‘clusters’ of CGIs according to their patterns of DNA methylation; the stably hypomethylated CGI cluster (cluster I), sperm-hypomethylated CGI cluster (cluster II), and variably methylated CGI cluster (cluster III). These epigenomic CGI clusters are strikingly distinct at multiple biological features including genomic, evolutionary, and functional characteristics. At the genomic level, the stably hypomethylated CGI cluster tends to be longer and harbors many more CpG dinucleotides than those in other clusters. They are also frequently associated with promoters, while CGI clusters II and III mostly reside in intragenic or intergenic regions and exhibit highly tissue-specific DNA methylation. Functional ontology terms and transcriptional profiles co-vary with CGI clusters, indicating that the regulatory functions of CGIs are tightly linked to their heterogeneity. Finally, CGIs associated with distinctive biological processes, such as diseases, aging, and imprinting, occur disproportionately across CGI clusters. These new findings provide an effective means to combine existing knowledge on CGIs into a genomic context while bringing new insights that elucidate the significance of DNA methylation across different biological conditions and demography.

New Light Is Shed on the Enigmatic Origin of the Lung Myofibroblast

New Light Is Shed on the Enigmatic Origin of the Lung Myofibroblast

Distinct sites of renal fibrosis in Crim1 mutant mice arise from multiple cellular origins

Crim1 is a transmembrane protein that regulates the bioavailability of growth factors such as VEGFA. Crim1(KST264)(/)(KST264) hypomorphic mice develop renal disease characterized by glomerular cysts and loss of endothelial integrity, progressing to peritubular and pericystic fibrosis. Peritubular capillary endothelial cells display morphological changes as well as detachment from the basement membrane. In this study, gene expression profiling of CD31(+) endothelial cells isolated from Crim1(KST264)(/)(KST264) kidneys showed up-regulation of transcripts associated with fibrosis (Col3a1, Loxl1), endothelial dysfunction (Abp1, Dcn, Lcn2), biomarkers of renal damage (Lcn2, Havcr1/Kim1) as well as evidence for a TGFβ1/TNF-associated inflammatory process. To determine whether the aberrant endothelium may in part contribute to the fibrogenic process, Tie2Cre-DsRed lineage tracing was undertaken in Crim1(KST264/KST264) mice. Approximately 31% of de novo αSMA(+) myofibroblasts detected within the tubulointerstitium were Tie2(+) DsRed(+) . However, 5.3% were F4/80(+) DsRed(+) , indicating a small population of myofibroblasts of monocytic rather than endothelial origin. In contrast, only 12% of myofibroblasts located around glomerular cysts were Tie2(+) DsRed(+) , with 7.7% being monocyte-derived (F4/80(+) DsRed(+) ). Collectively, this model supports the involvement of endothelial cells/monocytes in fibrosis within the tubulointerstitium, but also the heterogeneity of the fibrotic process even within distinct regions of the same kidney.

Roles of apolipoprotein E4 (ApoE4) in the pathogenesis of Alzheimer's disease: lessons from ApoE mouse models

ApoE4 (apolipoprotein E4) is the major known genetic risk factor for AD (Alzheimer's disease). In most clinical studies, apoE4 carriers account for 65-80% of all AD cases, highlighting the importance of apoE4 in AD pathogenesis. Emerging data suggest that apoE4, with its multiple cellular origins and multiple structural and biophysical properties, contributes to AD in multiple ways either independently or in combination with other factors, such as Aβ (amyloid β-peptide) and tau. Many apoE mouse models have been established to study the mechanisms underlying the pathogenic actions of apoE4. These include transgenic mice expressing different apoE isoforms in neurons or astrocytes, those expressing neurotoxic apoE4 fragments in neurons and human apoE isoform knock-in mice. Since apoE is expressed in different types of cells, including astrocytes and neurons, and in brains under diverse physiological and/or pathophysiological conditions, these apoE mouse models provide unique tools to study the cellular source-dependent roles of apoE isoforms in neurobiology and in the pathogenesis of AD. They also provide useful tools for discovery and development of drugs targeting apoE4's detrimental effects.

Mechanisms linking apolipoprotein E isoforms with cardiovascular and neurological diseases

The purpose of this review is to provide insights into recent advances in mechanisms linking apolipoprotein (apo) E isoforms to cardiovascular and neurological diseases. Human apoE has three common isoforms (apoE2, apoE3, and apoE4) with different structural and biophysical properties and different effects on lipid and neuronal homeostasis. ApoE is a protein constituent of different plasma lipoproteins and serves as a high-affinity ligand for several receptors. By interacting with its receptors, apoE mediates the clearance of different lipoproteins from the circulation. Absence or structural mutations of apoE cause significant disorders in lipid metabolism and cardiovascular disease. ApoE also has significant roles in neurobiology. ApoE4 is the major known genetic risk factor for Alzheimer's disease. It increases the occurrence and lowers the age of onset of Alzheimer's disease. ApoE4 carriers account for 65-80% of all Alzheimer's disease cases, highlighting the importance of apoE4 in Alzheimer's disease pathogenesis. ApoE4 has both amyloid beta-dependent and amyloid beta-independent roles in Alzheimer's disease pathogenesis. Emerging data suggest that apoE isoforms, with their multiple cellular origins and multiple structural and biophysical properties, contribute to cardiovascular and neurological diseases by interacting with different factors through various pathways.

Cellular Source of Apolipoprotein E4 Determines Neuronal Susceptibility to Excitotoxic Injury in Transgenic Mice

The lipid transport protein apolipoprotein E (apoE) is abundantly expressed in the brain. Its main isoforms in humans are apoE2, apoE3, and apoE4. ApoE4 is the major known genetic risk factor for Alzheimer's disease and also contributes to the pathogenesis of various other neurological conditions. In the central nervous system, apoE is synthesized by glial cells and neurons, but it is unclear whether the cellular source affects its biological activities. To address this issue, we induced excitotoxic injury by systemic kainic acid injection in transgenic Apoe knockout mice expressing human apoE isoforms in astrocytes or neurons. Regardless of its cellular source, apoE3 expression protected neuronal synapses and dendrites against the excitotoxicity seen in apoE-deficient mice. Astrocyte-derived apoE4, which has previously been shown to have detrimental effects in vitro, was as excitoprotective as apoE3 in vivo. In contrast, neuronal expression of apoE4 was not protective and resulted in loss of cortical neurons after excitotoxic challenge, indicating that neuronal apoE4 promotes excitotoxic cell death. Thus, an imbalance between astrocytic (excitoprotective) and neuronal (neurotoxic) apoE4 expression may increase susceptibility to diverse neurological diseases involving excitotoxic mechanisms.

A CreER-Based Random Induction Strategy for Modeling Translocation-Associated Sarcomas in Mice

Previously, we reported modeling synovial sarcomas in mice by conditionally expressing the human t(X;18) translocation-derived SYT-SSX2 fusion protein in Myf5-expressing myoblasts. Using a tamoxifen-inducible CreER system in mice, we show here that sporadic expression of SYT-SSX2 across multiple tissue types leads to exclusive formation of synovial sarcoma-like tumors, whereas its widespread expression is lethal. Certain clinical and histologic features of tumors in this new model suggest additional nonmyoblast origin for synovial sarcoma. CreER-based sporadic expression both avoids the severe early developmental phenotypes associated with widespread SYT-SSX2 expression and better models natural pathogenesis of cancers in which transformed cells usually arise within an environment of largely normal cells. Furthermore, this strategy may recapitulate multiple potential cellular origins within a single model system.