General Research Interests

Respiratory diseases are leading causes of death and disability in the world. Globally, four million people die prematurely from chronic respiratory diseases that includes lung cancer, chronic obstructive pulmonary disease (COPD), asthma, occupational lung diseases and pulmonary hypertension (PH). Exposure to harsh environments (indoor and outdoor pollutants, tobacco smoke, high-altitude dwelling and others) are the indisputable cause of most respiratory diseases. However, how these distinct environments (external, internal as well as local lung exposome) interact and modulate the parenchymal / vascular lung compartment that eventually leads to lung disease pathogenesis is not completely understood. Notably, a more holistic understanding of (epi)genome-exposome interaction and its impact on diagnosis and individualized therapy management is still in its infancy. The focus of Prof. Pullamsetti’s lab is centered on understanding how epigenetic mechanisms and transcription factors impact gene regulation so that this information can potentially be used to develop new therapeutic strategies for lung diseases especially. PH, pulmonary fibrosis and COPD.

Over the past several years, Pullamsetti lab has substantially contributed to the understanding of molecular mechanisms driving vascular and parenchymal remodeling. We identified growth factor and inflammatory networks; delineated their downstream effectors like FOXO, HIF and NFkB, thus demonstrating their importance in pulmonary hypertension (PH) onset and development. In seminal studies, smooth muscle cell FoxO1 was identified as critical integrator of multiple signaling pathways. -Hence in PH, dysregulation of FOXO1 drives the phenotypic switch of smooth muscle cells to a more proliferative type leading to subsequent lung vascular remodeling. Notably, reconstitution of FoxO1 activity reversed lung vascular remodeling, a concept carried forward to the current (pre)-clinical development of nanoparticle-based inhaled paclitaxel as a novel approach for the treatment of PH. Furthermore, employing the “integromic” approaches, i.e. studying the combination of epigenetic and transcriptional changes, helps to elucidate disease-specific transcriptional and epigenetic landscape changes thus leading to the identification potential targets for the reversal of disease phenotypes. Completing this approach, Pullamsetti lab has also mapped out abnormalities of non-coding RNAs and of histone- and non-histone mediated functions of histone modifiers linked with the pathobiology of PH thus directing the focus to the evaluation of the therapeutic efficacy of histone acetylation / deacetylation inhibitors in PH.

Extending the studies of gene regulatory networks and epigenomics to understand lung diseases, Pullamsetti lab also identified and documented an important role of nitric oxide signaling in alveolar epithelial cells. This group also discovered that FoxO3 plays a central role in regulating multiple signaling pathways in parenchymal fibroblasts from experimental models of lung fibrosis and also from tissue samples of patients with IPF (idiopathic lung fibrosis) and eventually identified histone deacetylases (HDAC9) as a master regulator of lung fibrogenesis. Another discovery was an association of clonal hematopoiesis of indeterminate potential (CHIP) and DNA methylation correlated with inflammatory gene expression in patients with COPD.

Based on these findings, the Pullamsetti lab will focus on:

Multiomics and Epigenetic landscape

Dr. Prakash Chelladurai, Fatemeh Khassafi, Nassima Mordjana, Leili Jafari, Samuel Olapoju

Epigenetic mechanisms, including DNA accessibility, histone modifications, DNA methylation and non-coding RNAs, regulate gene expression and translation and thereby modify cell phenotype and function. Moreover, epigenetic changes act as mediators of the interaction between environmental factors (hypoxia, infection, smoke, physical activity etc.) and genetic factors. Hence, epigenome-focused therapies represent a novel arena for the development of lung health preserving and restoring therapies. Against this background, Pullamsetti lab will focus on epigenomic profiling of different lung cells to understand their phenotypic/metabolic/functional heterogeneity in pathological vascular and parenchymal remodeling events, as occurring in various lung diseases (see overview figure). Importantly, generating cell-type specific transcriptomic and epigenomic maps at single-cell resolution is crucial to understand the cell-state transitions and the cellular cross talk between epithelial, endothelial, fibroblast-type and smooth muscle cells, including their resident stem/progenitor cells, as well as infiltrating bone marrow-derived immune and progenitor cells. To this end, this group has established and will further extend single-cell and single-nuclei preparation protocols for experimental and human lung tissue. In order to define the cellular composition and phenotypic heterogeneity of novel subpopulations, isolated cells will be sorted by flow activated cell sorting and subjected to gene expression profiling using single-cell or single-nuclei RNA sequencing (scRNA-seq, snRNA-seq), and studying chromatin accessibility using microfluidics-based single-cell assays for transposase-accessible chromatin (scATAC-seq). Multi-omic analysis of corresponding scRNA-seq and scATAC-seq datasets will be performed to map cellular identities and subclusters and their respective molecular signatures. Results of this “integromic” approach will be linked with architectural and functional pulmonary abnormalities in various lung diseases. Furthermore, these studies will be extended to nucleosome epigenetic features including histone and DNA modifications as well as histone variants or nucleosome adducts, representing a further level of complexity. We expect that these studies will substantially advance our knowledge of the “deep” genomic/gene regulatory events governing lung health maintenance and disease development, leading to the identification of new classes of diagnostic and prognostic biomarkers and “epigenome-focused therapies”. We hope all these studies will offer new approaches for preserving and restoring lung health beyond currently available therapies.

Aging and CHIP

Edibe Avci, Siavash Mansouri, Dr. Manju Padmasekhar, Dr. Prakash Chelladurai

Aging is the main risk factor for major non-communicable chronic lung diseases, including chronic obstructive pulmonary disease, most forms of lung fibrosis and lung cancer. A series of recent finding suggest that epigenetic mechanisms might be involved in the regulation of aging-related gene expression. Moreover, aging is associated with increased number of somatic mutations in tissues, including the hematopoietic system. Somatic mutations in epigenetic modifiers and transcription factors of hematopoietic stem cells results in clonal outgrowth of a mutant population of blood cells in individuals without a clinical manifestation of hematologic malignancy, termed as Clonal hematopoiesis of indeterminate potential (CHIP). Patients with CHIP display an aberrant inflammatory response and an elevated risk for cardiovascular diseases, but the association of CHIP with chronic lung diseases is not yet understood and is a promising research area.

We have observed an association between COPD and increased somatic mutations in hematopoietic cells, specifically, in the most commonly mutated CHIP driver gene DNMT3A. This association could drive the abnormal lipid and inflammatory sequelae in COPD and hence the functional outcome. Lung insults such as smoking or the lung disease itself may enhance the CHIP frequency in the bone marrow stem cell niche which then - as a vicious feedback loop – may amplify the pulmonary pathogenetic sequelae. Our group would like to continue to study how alterations in epigenetic modifiers alter the lung and lung vasculature aging and the underlying molecular mechanisms. In addition, we aim to investigate the prevalence of CHIP in patients with lung diseases, evaluate CHIP mediated molecular consequences by performing epigenomic, metabolomics and cytokine analyses and correlate the data with lung function parameters. The causality of CHIP on inflammation will be evaluated in macrophages derived from human peripheral blood mononuclear cells.

LncRNAs and RNA modifications

Dr. Chanil Valasarajan, Dr. Giovanni Maroli, Zahraa Msheik, Prabhdeep Singh Gothra

Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs, specifically >200 nucleotides in length, and act as key signalling modulators and drivers of various molecular pathways as evident from several studies. Functionally, they act as decoys of chromatin modifiers, as microRNA sponge, or scaffolds in ribonucleo-protein complexes thus by regulating signalling pathways. During the last years, the field of RNA therapeutics has gained immense attention with the development of mRNA vaccines against various diseases including COVID-19. Considering the pivotal role of lncRNAs in regulating various biological processes, lncRNA based therapies represent a promising therapeutic approach, especially for diseases with poor treatment options such as PH. Employing sequencing approaches, our group has identified deregulated lncRNAs in hypoxia exposed human pulmonary arterial smooth muscle cells and lung pericytes and also from patient samples with idiopathic PAH that exhibit a hyperproliferative and apoptosis-resistant phenotype. Importantly, we identified a novel lncRNA, TYKRIL (tyrosine kinase receptor–inducing lncRNA), which is a checkpoint molecule in p53/PDGFRβ (platelet-derived growth factor receptor β) signaling with functional relevance in both hyperproliferating pulmonary artery smooth muscle cells and pericytes, suggesting that it may serve as a novel therapeutic target in PH.

Based on these findings, we would like to assess the spatiotemporal regulation of lncRNAs upon distinct environmental exposures. Understanding how lncRNAs regulate major signaling pathways thus regulating lung vascular and parenchymal cellular phenotypes will play a pivotal role in developing lncRNA based therapeutic strategies for lung diseases.

In addition, we aim to explore the role of post-transcriptional modifications of RNA in lung pathogenesis. We will specifically focus on the role of RNA editing, which is predominantly mediated by adenosine and cytidine deaminases acting on DNA and RNA. Preliminary results from our lab suggest a dysregulation of the Adar1/MDA5/ISGs axis in pulmonary arterial smooth muscle cells isolated from PH patients. We thus aim to investigate the roles of RNA editing mediated signaling in the lung vasculature which might play a role in tissue remodeling in PH.

Transcription factors

Dr. Anoop Cherian, Sreenath Nayakanti, Dr. Giovanni Maroli, Michele Ebeling

Transcription factors (TFs) are convergence points of signaling cascades that coordinate cell differentiation, proliferation, survival, and migration; and are commonly deregulated in various lung diseases. Our group identified the roles of TFs/TF co-regulators FOXO, HIF and ß-Catenin and demonstrated their importance in pulmonary hypertension and lung fibrosis onset and development. In preliminary studies, smooth muscle cell FoxO1 was identified as critical integrator of multiple signaling pathways, driving a phenotypic switch of these cells leading to subsequent lung vascular remodeling, whereas FoxO3 plays a crucial role in parenchymal remodeling. Notably, reconstitution of FoxO1 activity reversed lung vascular remodeling, a concept carried forward to the current (pre)-clinical development of nanoparticle-based inhaled Paclitaxel as novel approach for the treatment of PH. In addition, this group has identified a hitherto unknown feed-forward loop between RASSF1A (scaffold protein) and HIF-1α, promoting metabolic reprogramming and glycolytic shift in hypoxia-exposed lung vascular cells, a mechanism overlapping with central features of cancer biology. Moreover, we have identified re-activation of lung developmental transcription factors such as T-box family (TBX) and SOX transcription factors in adult “remodeled” lung vasculature in human PH and animal models of PH.

Our group will continue to explore the TF driven molecular mechanisms during homeostasis and physiological or pathological perturbations - e.g.in pulmonary vascular and in right ventricular remodeling. Topics of special interest include:

To study the interplay between specific transcription factors (e.g. FOXOs, TBXs, HIFs) and proteins implicated in transcriptional regulation of a relevant gene and modulating 3D chromatin architecture in promoting tissue-specific chromatin interactions in response to external stimuli. We also aim to study the potential role of TFs (FOXOs, TBXs, HIFs) and cooperative interactions between these TFs in driving the postnatal pulmonary vascular adaptation in persistent PH of the newborn and adult PH. Furthermore, we aim to determine the epigenetic landscape of TFs circuitry during physiological development, pathological remodeling and in reverse remodeling and plan harness this knowledge to reverse pathological remodeling.

Reverse remodeling and regenerative therapies

Dr. Manju Padmasekhar, Golnaz Hessami, Dr. Chanil Valasarajan

Drugs which are available to-date to treat lung diseases has only modest effects on clinical end points while morbidity and mortality are still high. Limited availability of donor lungs also makes lung transplantation a remote possibility for end-stage lung diseases. This situation warrants further research into finding appropriate therapeutic alternatives which aims not only at treating the symptoms but also at preventing progression and/or reverse vascular and parenchymal pathology. Hence, the search for molecules, signaling pathways and cells that can contribute to the process of lung regeneration and repair has been fueled by the need for improved clinical therapies to treat lung diseases. In our lab, we aim to reverse vascular pathology and regenerate diseased PH lungs by employing a multi-strategic approach, i.e. identifying and targeting master TFs, lncRNAs and epigenetic modulators and improvising therapeutic modalities like:

As well as applying models of higher translational potential such as:

© 2021 PULLAMSETTI LAB || Center for Infection and Genomics of the Lung (CIGL), Justus-Liebig-Universität Gießen.