Research

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12 pages, 2941 KiB

Open AccessArticle

The Overlooked Microbiome—Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes

by Carolin Baehren, Anton Pembaur, Patrick P. Weil, Nora Wewers, Frank Schult, Stefan Wirth, Jan Postberg and Malik Aydin

Int. J. Mol. Sci. 2023, 24(2), 1426; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24021426 - 11 Jan 2023

Cited by 1 | Viewed by 2200

Abstract

In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the [...] Read more.

In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol’s broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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18 pages, 3789 KiB

Open AccessArticle

Hedgehog Signaling Pathway Orchestrates Human Lung Branching Morphogenesis

by Randa Belgacemi, Soula Danopoulos, Gail Deutsch, Ian Glass, Valérian Dormoy, Saverio Bellusci and Denise Al Alam

Int. J. Mol. Sci. 2022, 23(9), 5265; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23095265 - 09 May 2022

Cited by 6 | Viewed by 2531

Abstract

The Hedgehog (HH) signaling pathway plays an essential role in mouse lung development. We hypothesize that the HH pathway is necessary for branching during human lung development and is impaired in pulmonary hypoplasia. Single-cell, bulk RNA-sequencing data, and human fetal lung tissues were [...] Read more.

The Hedgehog (HH) signaling pathway plays an essential role in mouse lung development. We hypothesize that the HH pathway is necessary for branching during human lung development and is impaired in pulmonary hypoplasia. Single-cell, bulk RNA-sequencing data, and human fetal lung tissues were analyzed to determine the spatiotemporal localization of HH pathway actors. Distal human lung segments were cultured in an air-liquid interface and treated with an SHH inhibitor (5E1) to determine the effect of HH inhibition on human lung branching, epithelial-mesenchymal markers, and associated signaling pathways in vitro. Our results showed an early and regulated expression of HH pathway components during human lung development. Inhibiting HH signaling caused a reduction in branching during development and dysregulated epithelial (SOX2, SOX9) and mesenchymal (ACTA2) progenitor markers. FGF and Wnt pathways were also disrupted upon HH inhibition. Finally, we demonstrated that HH signaling elements were downregulated in lung tissues of patients with a congenital diaphragmatic hernia (CDH). In this study, we show for the first time that HH signaling inhibition alters important genes and proteins required for proper branching of the human developing lung. Understanding the role of the HH pathway on human lung development could lead to the identification of novel therapeutic targets for childhood pulmonary diseases. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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Review

Jump to: Research

20 pages, 973 KiB

Open AccessReview

Stem/Progenitor Cells and Related Therapy in Bronchopulmonary Dysplasia

by Manuela Marega, Natalia El-Merhie, Mira Y. Gökyildirim, Valerie Orth, Saverio Bellusci and Cho-Ming Chao

Int. J. Mol. Sci. 2023, 24(13), 11229; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241311229 - 07 Jul 2023

Cited by 2 | Viewed by 1685

Abstract

Bronchopulmonary dysplasia (BPD) is a chronic lung disease commonly seen in preterm infants, and is triggered by infection, mechanical ventilation, and oxygen toxicity. Among other problems, lifelong limitations in lung function and impaired psychomotor development may result. Despite major advances in understanding the [...] Read more.

Bronchopulmonary dysplasia (BPD) is a chronic lung disease commonly seen in preterm infants, and is triggered by infection, mechanical ventilation, and oxygen toxicity. Among other problems, lifelong limitations in lung function and impaired psychomotor development may result. Despite major advances in understanding the disease pathologies, successful interventions are still limited to only a few drug therapies with a restricted therapeutic benefit, and which sometimes have significant side effects. As a more promising therapeutic option, mesenchymal stem cells (MSCs) have been in focus for several years due to their anti-inflammatory effects and their secretion of growth and development promoting factors. Preclinical studies provide evidence in that MSCs have the potential to contribute to the repair of lung injuries. This review provides an overview of MSCs, and other stem/progenitor cells present in the lung, their identifying characteristics, and their differentiation potential, including cytokine/growth factor involvement. Furthermore, animal studies and clinical trials using stem cells or their secretome are reviewed. To bring MSC-based therapeutic options further to clinical use, standardized protocols are needed, and upcoming side effects must be critically evaluated. To fill these gaps of knowledge, the MSCs’ behavior and the effects of their secretome have to be examined in more (pre-) clinical studies, from which only few have been designed to date. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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10 pages, 1040 KiB

Open AccessReview

SOX2 and SOX21 in Lung Epithelial Differentiation and Repair

by Evelien Eenjes, Dick Tibboel, Rene M. H. Wijnen, Johannes Marco Schnater and Robbert J. Rottier

Int. J. Mol. Sci. 2022, 23(21), 13064; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232113064 - 27 Oct 2022

Cited by 2 | Viewed by 1931

Abstract

The lung originates from the ventral foregut and develops into an intricate branched structure of airways, alveoli, vessels and support tissue. As the lung develops, cells become specified and differentiate into the various cell lineages. This process is controlled by specific transcription factors, [...] Read more.

The lung originates from the ventral foregut and develops into an intricate branched structure of airways, alveoli, vessels and support tissue. As the lung develops, cells become specified and differentiate into the various cell lineages. This process is controlled by specific transcription factors, such as the SRY-related HMG-box genes SOX2 and SOX21, that are activated or repressed through intrinsic and extrinsic signals. Disturbances in any of these processes during the development of the lung may lead to various pediatric lung disorders, such as Congenital Diaphragmatic Hernia (CDH), Congenital Pulmonary Airway Malformation (CPAM) and Broncho-Pulmonary Dysplasia (BPD). Changes in the composition of the airways and the alveoli may result in reduced respiratory function and eventually lead to chronic lung disorders. In this concise review, we describe different intrinsic and extrinsic cellular processes required for proper differentiation of the epithelium during development and regeneration, and the influence of the microenvironment on this process with special focus on SOX2 and SOX21. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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13 pages, 1737 KiB

Open AccessReview

The Role of Insulin Receptor Substrate Proteins in Bronchopulmonary Dysplasia and Asthma: New Potential Perspectives

by Gokhan Gorgisen, Malik Aydin, Olivier Mboma, Mira Y. Gökyildirim and Cho-Ming Chao

Int. J. Mol. Sci. 2022, 23(17), 10113; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231710113 - 04 Sep 2022

Cited by 1 | Viewed by 1998

Abstract

Insulin receptor substrates (IRSs) are proteins that are involved in signaling through the insulin receptor (IR) and insulin-like growth factor (IGFR). They can also interact with other receptors including growth factor receptors. Thus, they represent a critical node for the transduction and regulation [...] Read more.

Insulin receptor substrates (IRSs) are proteins that are involved in signaling through the insulin receptor (IR) and insulin-like growth factor (IGFR). They can also interact with other receptors including growth factor receptors. Thus, they represent a critical node for the transduction and regulation of multiple signaling pathways in response to extracellular stimuli. In addition, IRSs play a central role in processes such as inflammation, growth, metabolism, and proliferation. Previous studies have highlighted the role of IRS proteins in lung diseases, in particular asthma. Further, the members of the IRS family are the common proteins of the insulin growth factor signaling cascade involved in lung development and disrupted in bronchopulmonary dysplasia (BPD). However, there is no study focusing on the relationship between IRS proteins and BPD yet. Unfortunately, there is still a significant gap in knowledge in this field. Thus, in this review, we aimed to summarize the current knowledge with the major goal of exploring the possible roles of IRS in BPD and asthma to foster new perspectives for further investigations. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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28 pages, 955 KiB

Open AccessReview

Insights into the Black Box of Intra-Amniotic Infection and Its Impact on the Premature Lung: From Clinical and Preclinical Perspectives

by Ying Dong, Stefano Rivetti, Arun Lingampally, Sabine Tacke, Baktybek Kojonazarov, Saverio Bellusci and Harald Ehrhardt

Int. J. Mol. Sci. 2022, 23(17), 9792; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23179792 - 29 Aug 2022

Cited by 3 | Viewed by 2004

Abstract

Intra-amniotic infection (IAI) is one major driver for preterm birth and has been demonstrated by clinical studies to exert both beneficial and injurious effects on the premature lung, possibly due to heterogeneity in the microbial type, timing, and severity of IAI. Due to [...] Read more.

Intra-amniotic infection (IAI) is one major driver for preterm birth and has been demonstrated by clinical studies to exert both beneficial and injurious effects on the premature lung, possibly due to heterogeneity in the microbial type, timing, and severity of IAI. Due to the inaccessibility of the intra-amniotic cavity during pregnancies, preclinical animal models investigating pulmonary consequences of IAI are indispensable to elucidate the pathogenesis of bronchopulmonary dysplasia (BPD). It is postulated that on one hand imbalanced inflammation, orchestrated by lung immune cells such as macrophages, may impact on airway epithelium, vascular endothelium, and interstitial mesenchyme, resulting in abnormal lung development. On the other hand, excessive suppression of inflammation may as well cause pulmonary injury and a certain degree of inflammation is beneficial. So far, effective strategies to prevent and treat BPD are scarce. Therapeutic options targeting single mediators in signaling cascades and mesenchymal stromal cells (MSCs)-based therapies with global regulatory capacities have demonstrated efficacy in preclinical animal models and warrant further validation in patient populations. Ante-, peri- and postnatal exposome analysis and therapeutic investigations using multiple omics will fundamentally dissect the black box of IAI and its effect on the premature lung, contributing to precisely tailored and individualized therapies. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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23 pages, 736 KiB

Open AccessReview

Pathophysiological Concepts and Management of Pulmonary Manifestation of Pediatric Inflammatory Bowel Disease

by Florian Schmid, Cho-Ming Chao and Jan Däbritz

Int. J. Mol. Sci. 2022, 23(13), 7287; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23137287 - 30 Jun 2022

Cited by 3 | Viewed by 2451

Abstract

Pulmonary manifestation (PM) of inflammatory bowel disease (IBD) in children is a rare condition. The exact pathogenesis is still unclear, but several explanatory concepts were postulated and several case reports in children were published. We performed a systematic Medline search between April 1976 [...] Read more.

Pulmonary manifestation (PM) of inflammatory bowel disease (IBD) in children is a rare condition. The exact pathogenesis is still unclear, but several explanatory concepts were postulated and several case reports in children were published. We performed a systematic Medline search between April 1976 and April 2022. Different pathophysiological concepts were identified, including the shared embryological origin, “miss-homing” of intestinal based neutrophils and T lymphocytes, inflammatory triggering via certain molecules (tripeptide proline-glycine-proline, interleukin 25), genetic factors and alterations in the microbiome. Most pediatric IBD patients with PM are asymptomatic, but can show alterations in pulmonary function tests and breathing tests. In children, the pulmonary parenchyma is more affected than the airways, leading histologically mainly to organizing pneumonia. Medication-associated lung injury has to be considered in pulmonary symptomatic pediatric IBD patients treated with certain agents (i.e., mesalamine, sulfasalazine or infliximab). Furthermore, the risk of pulmonary embolism is generally increased in pediatric IBD patients. The initial treatment of PM is based on corticosteroids, either inhaled for the larger airways or systemic for smaller airways and parenchymal disease. In summary, this review article summarizes the current knowledge about PM in pediatric IBD patients, focusing on pathophysiological and clinical aspects. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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29 pages, 1142 KiB

Open AccessReview

Respiratory and Intestinal Microbiota in Pediatric Lung Diseases—Current Evidence of the Gut–Lung Axis

by Sebastian Stricker, Torsten Hain, Cho-Ming Chao and Silvia Rudloff

Int. J. Mol. Sci. 2022, 23(12), 6791; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23126791 - 18 Jun 2022

Cited by 13 | Viewed by 4147

Abstract

The intestinal microbiota is known to influence local immune homeostasis in the gut and to shape the developing immune system towards elimination of pathogens and tolerance towards self-antigens. Even though the lung was considered sterile for a long time, recent evidence using next-generation [...] Read more.

The intestinal microbiota is known to influence local immune homeostasis in the gut and to shape the developing immune system towards elimination of pathogens and tolerance towards self-antigens. Even though the lung was considered sterile for a long time, recent evidence using next-generation sequencing techniques confirmed that the lower airways possess their own local microbiota. Since then, there has been growing evidence that the local respiratory and intestinal microbiota play a role in acute and chronic pediatric lung diseases. The concept of the so-called gut–lung axis describing the mutual influence of local microbiota on distal immune mechanisms was established. The mechanisms by which the intestinal microbiota modulates the systemic immune response include the production of short-chain fatty acids (SCFA) and signaling through pattern recognition receptors (PRR) and segmented filamentous bacteria. Those factors influence the secretion of pro- and anti-inflammatory cytokines by immune cells and further modulate differentiation and recruitment of T cells to the lung. This article does not only aim at reviewing recent mechanistic evidence from animal studies regarding the gut–lung axis, but also summarizes current knowledge from observational studies and human trials investigating the role of the respiratory and intestinal microbiota and their modulation by pre-, pro-, and synbiotics in pediatric lung diseases. Full article

(This article belongs to the Special Issue Pediatric Lung Diseases: Novel Molecular Insights and Therapeutic Advances)

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