Biology subjects

Rajan, S.

Publications and source records attributed to Rajan, S..

6 recordsLinked to original sources

bioRxiv2021

Remarkably stable copy-number profiles in osteosarcoma revealed using single-cell DNA sequencing

Osteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNAs) are the genetic drivers of disease. Models around genomic instability conflict - it is unclear if osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in >12,000 tumor cells obtained from human osteosarcomas using single cell DNA sequencing, with a degree of precision and accuracy not possible when inferring single cell states using bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from this whole-genome single cell DNA sequencing data. Surprisingly, despite extensive structural complexity, these tumors exhibit a high degree of cell-cell homogeneity with little sub-clonal diversification. Longitudinal analysis of patient samples obtained at distant therapeutic time points (diagnosis, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the majority of SCNAs were acquired early in the oncogenic process, with relatively few structure-altering events arising in response to therapy or during adaptation to growth in metastatic tissues. These data further support the emerging hypothesis that early catastrophic events, rather than sustained genomic instability, give rise to structural complexity, which is then preserved over long periods of tumor developmental time. Significance StatementChromosomally complex tumors are often described as genomically unstable. However, determining whether complexity arises from remote time-limited events that give rise to structural alterations or a progressive accumulation of structural events in persistently unstable tumors has implications for diagnosis, biomarker assessment, mechanisms of treatment resistance, and represents a conceptual advance in our understanding of intra-tumoral heterogeneity and tumor evolution.

cancer biology↗

bioRxiv2021

dsMTL - a computational framework for privacy-preserving, distributed multi-task machine learning

Multitask learning allows the simultaneous learning of multiple communicating algorithms. It is increasingly adopted for biomedical applications, such as the modeling of disease progression. As data protection regulations limit data sharing for such analyses, an implementation of multitask learning on geographically distributed data sources would be highly desirable. Here, we describe the development of dsMTL, a computational framework for privacy-preserving, distributed multi-task machine learning that includes three supervised and one unsupervised algorithms. dsMTL is implemented as a library for the R programming language and builds on the DataSHIELD platform that supports the federated analysis of sensitive individual-level data. We provide a comparative evaluation of dsMTL for the identification of biological signatures in distributed datasets using two case studies, and evaluate the computational performance of the supervised and unsupervised algorithms. dsMTL provides an easy- to-use framework for privacy-preserving, federated analysis of geographically distributed datasets, and has several application areas, including comorbidity modeling and translational research focused on the simultaneous prediction of different outcomes across datasets. dsMTL is available at https://github.com/transbioZI/dsMTLBase (server-side package) and https://github.com/transbioZI/dsMTLClient (client-side package).

bioinformatics↗

bioRxiv2020

Osteosarcoma tumors maintain intertumoral heterogeneity, even while adapting to environmental pressures that drive clonal selection

BackgroundTumors are complex tissues containing collections of phenotypically diverse malignant and nonmalignant cells. We know little of the mechanisms that govern heterogeneity of tumor cells nor of the role heterogeneity plays in overcoming stresses, such as adaptation to different microenvironments. Osteosarcoma is an ideal model for studying these mechanisms--it exhibits widespread inter- and intra-tumoral heterogeneity, predictable patterns of metastasis, and a lack of clear targetable driver mutations. Understanding the processes that facilitate adaptation to primary and metastatic microenvironments could inform the development of therapeutic targeting strategies. ResultsWe investigated single-cell RNA-sequencing profiles of 47,977 cells obtained from cell line and patient-derived xenograft models as cells adapted to growth within primary bone and metastatic lung environments. Tumor cells maintained phenotypic heterogeneity as they responded to the selective pressures imposed during bone and lung colonization. Heterogenous subsets of cells defined by distinct transcriptional profiles were maintained within bone- and lung-colonizing tumors, despite high-level selection. One prominent heterogenous feature involving glucose metabolism was clearly validated using immunofluorescence staining. Finally, using concurrent lineage tracing and single-cell transcriptomics, we found that lung colonization enriches for multiple clones with distinct transcriptional profiles that are preserved across cellular generations. ConclusionsResponse to environmental stressors occurs through complex and dynamic phenotypic adaptations. Heterogeneity is maintained, even in conditions that enforce clonal selection. These findings likely reflect the influences of developmental processes promoting diversification of tumor cell subpopulations, which are retained, even in the face of selective pressures.

cancer biology↗

bioRxiv2019

Transient receptor vanilloid 4 (TRPV4) channels are essential for alveolar epithelial cell function

Ischemia-reperfusion(IR)-induced edema formation can be mimicked ex-vivo in isolated perfused mouse lungs (IPL). Here we show enhanced edema formation in transient receptor potential vanilloid 4 (TRPV4)-deficient (TRPV4-/-) IPL compared to wild-type (WT) controls in response to IR, indicating a protective role of TRPV4 to maintain the alveolar epithelial barrier. By immunohistochemistry, mRNA profiling or electrophysiological analysis we detected TRPV4 in bronchial epithelium, alveolar type I (ATI) and alveolar type II (ATII) cells. Genetic ablation of TRPV4 resulted in reduced expression of aquaporin-5 (AQP-5) channels in ATI as well as decreased production of pro surfactant protein C (pSP-C) in ATII cells. Migration of TRPV4-deficient ATI cells was reduced and cell barrier function was impaired. Moreover, adult TRPV4-/- lungs developed emphysema-like changes and altered lung parameters compared to WT lungs. Therefore, our data highlight novel essential functions of TRPV4 channels in alveolar epithelial cells and in the protection from edema formation.\n\neLife digestTransient receptor potential vanilloid 4 (TRPV4) is a non-selective Ca2+ permeable cation channel expressed in lung endothelium where increased channel activity has been shown to compromise endothelial barrier function. In other tissues however, the channel maintains physiological cell barriers, e.g. in skin, the urogenital tract and the corneal epithelium. In tracheal epithelial cells TRPV4 channels regulate ciliar beat frequency and in alveolar epithelial cells TRPV4 activation by 4-phorbol esters produced blebs and breaks in lung septa by unknown molecular mechanisms. To understand the channels role in lung function Weber et al. employed ex-vivo isolated perfused mouse lungs (IPL) to mimic ischemia-reperfusion-induced edema as one of the most common and significant causes of morbidity and mortality after lung transplantation in human patients. TRPV4-deficient (TRPV4-/-) IPL developed enhanced edema formation compared to wild-type (WT) controls in response to ischemia and reperfusion, indicating a protective role of TRPV4 to maintain the alveolar epithelial barrier. TRPV4 was detected in bronchial epithelium, alveolar type I (ATI) and alveolar type II (ATII) cells by immunohistochemistry or mRNA profiling. Genetic ablation of TRPV4 resulted in reduced expression and plasma membrane insertion of water conducting aquaporin-5 (AQP-5) channels in ATI cells compared to WT mice. Analysis of isolated primary TRPV4-/- ATII cells revealed a reduced expression of pro surfactant protein-C (pSP-C) a precursor of a protein important for decreasing surface tension and for alveolar fluid homeostasis. Moreover, the TRPV4 activator GSK1016790A induced increases in current densities only in WT but not in TRPV4-/- ATII cells. On a molecular level ablation of TRPV4 induced less Ca2+-mediated nuclear translocation of nuclear factor of activated T-cells (NFAT) to the nucleus, which may be responsible for reduced expression of the identified proteins. Although the ability of TRPV4-/- ATII to differentiate to ATI cells was unchanged, migration of TRPV4-deficient ATI cells was reduced and cell barrier function was impaired. Moreover, TRPV4-/- lungs of adult mice developed significantly larger mean chord lengths and altered lung function compared to WT lungs. The findings of Weber et al. highlights novel essential functions of TRPV4 channels in alveolar epithelial cells and in the protection from edema formation.

cell biology↗

bioRxiv2019

Sympatric wren-warblers partition acoustic signal space and song perch height

By evolving divergent acoustic signals, sympatric assemblages of animals may minimize potentially costly masking interference. Acoustic signal space may be multidimensional, with coexisting species also vocalizing from different regions of physical space. Here, we demonstrate acoustic signal space partitioning in four sympatric species of wren-warbler (Cisticolidae, Prinia), in an Indian dry deciduous scrub habitat. We find that the breeding songs of wren-warblers are divergent from each other in multivariate parameter space, with only minimal interspecific overlap. Partitioning of signal space exerts constraints on the intraspecific diversity of acoustic signals, and each species exhibits different strategies to overcome these constraints. Two species partition intraspecific signal space into multiple note types, whereas a third exhibits intraspecific variation in repetition rate, thus supporting song diversity within a constrained acoustic space. Finally, we find that the four species also partition song perch heights, thus exhibiting separation along multiple axes of acoustic signal space. We hypothesize that divergent song perch heights may be driven by competition for higher singing perches or other ecological factors rather than signal propagation. Acoustic signal partitioning along multiple axes may therefore, we propose, arise from a combination of diverse ecological processes.

animal behavior and cognition↗

bioRxiv2019

A missense mutation dissociates triglyceride and phospholipid transfer activities in zebrafish and human microsomal triglyceride transfer protein

Microsomal triglyceride transfer protein (MTP) transfers triglycerides and phospholipids and is essential for the assembly of Apolipoprotein B (ApoB)-containing lipoproteins in the endoplasmic reticulum. We have discovered a zebrafish mutant (mttpc655) expressing a C-terminal missense mutation (G863V) in Mttp, one of the two subunits of MTP, that is defective at transferring triglycerides, but retains phospholipid transfer activity. Mutagenesis of the conserved glycine in the human MTTP protein (G865V) also eliminates triglyceride but not phospholipid transfer activity. The G863V mutation reduces the production and size of ApoB-containing lipoproteins in zebrafish embryos and results in the accumulation of cytoplasmic lipid droplets in the yolk syncytial layer. However, mttpc655 mutants exhibit only mild intestinal lipid malabsorption and normal growth as adults. In contrast, zebrafish mutants bearing the previously identified mttpstl mutation (L475P) are deficient in transferring both triglycerides and phospholipids and exhibit gross intestinal lipid accumulation and defective growth. Thus, the G863V point mutation provides the first evidence that the triglyceride and phospholipid transfer functions of a vertebrate MTP protein can be separated, arguing that selective inhibition of the triglyceride transfer activity of MTP may be a feasible therapeutic approach for dyslipidemia.

physiology↗