Biology subjects

Sen, P.

Publications and source records attributed to Sen, P..

42 records · Page 3Linked to original sources

bioRxiv2021

Quantitative analysis and genome-scale modeling of human CD4+ T-cell differentiation reveals subset-specific regulation of glycosphingolipid pathways

T-cells are sentinels of adaptive cell-mediated immune responses. T-cell activation, proliferation and differentiation involves metabolic reprogramming involving the interplay of genes, proteins and metabolites. Here, we aim to understand the metabolic pathways involved in the activation and functional differentiation of human CD4+ T-cell subsets (Th1, Th2, Th17 and iTregs). We combined genome-scale metabolic modeling, gene expression data, targeted and non-targeted lipidomics experiments, together with in vitro gene knockdown experiments and showed that human CD4+ T-cells undergo specific metabolic changes during activation and functional differentiation. In addition, we identified and confirmed the importance of ceramide and glycosphingolipid synthesis pathways in Th17 differentiation and effector functions. Finally, through in vitro gene knockdown experiments, we substantiated the requirement of serine palmitoyl transferase (SPT), a de novo sphingolipid pathway in the expression of proinflammatory cytokine (IL17A and IL17F) by Th17 cells. Our findings may provide a comprehensive resource for identifying CD4+ T-cell-specific targets for their selective manipulation under disease conditions, particularly, diseases characterized by an imbalance of Treg / Th17 cells. Our data also suggest a role for elevated levels of ceramides in conditions comorbid with these diseases, e.g., obesity and insulin resistance.

immunology↗

bioRxiv2020

Vortex chip incorporating an orthogonal turn for size-based isolation of circulating cells

Label-free separation of rare cells (e.g. circulating tumor cells (CTCs)) based on their size is attractive due to its wider applicability, simpler sample preparation, faster turnaround, better efficiency and higher purity. Amongst cognate protocols for the same, vortex-trapping based techniques offer high throughput but operate at high flow velocities where the resulting hydrodynamic shear stress is likely to damage cells and compromise their viability for subsequent assays. We present here an orthogonal vortex chip which can carry out size-differentiated trapping at significantly lower (38% of previously reported) flow velocities. Fluid flowing through the chip is constrained to exit the trapping chamber at right angles to that of its entry. Such a flow configuration leads to the formation of vortex in the chamber. Above a critical flow velocity, larger particles are trapped in the vortex whereas smaller particles get ejected with the flow: we call this phenomenon the turn-effect. We have characterized the critical velocities for trapping of cells and particles of different sizes on chips with distinct entry-exit configurations. Optimal architectures for stable vortex trapping at low flow velocities are identified. We explain how shear-gradient lift, centrifugal and Dean flow drag forces contribute to the turn-effect by acting on cells which pushes them into specific vortices in a size- and velocity-dependent fashion. Finally, we demonstrate selective trapping of human breast cancer cells mixed with whole blood at low-concentration. Our findings suggest that the device shows promise for the gentle isolation of rare cells from blood.

bioengineering↗

bioRxiv2020

Highly accurate random DNA sequencing using inherent interlayer potential traps of bilayer MoS2 nanopores

Solid-state MoS2 nanopores are emerging as potential real-time DNA sequencers due to their ultra-thinness and pore stability. One of the major challenges in determining random nucleotide sequence (unlike polynucleotide strands) is the non-homogeneity of the charge interaction and velocity during DNA translocation. This results in varying blockade current for the same nucleotide, reducing the sequencing confidence. In this work, we studied the inherent impedance-tunability (due to vertical interlayer potential gradient and ion accumulation) of multilayered MoS2 nanopores along with its effect on improving analyte capture and charge interaction, for more sensitive and confident sensing. Experimentally we demonstrate that 2-3 nm diameter bilayer MoS2 pores are best suited for high accuracy (~90%) sequencing of mixed nucleotides with signal-to-noise-ratio greater than 11 in picomolar concentration solutions. High temporal resolution demonstrated by bilayer MoS2 nanopores can help detect neutral proteins in future. The high accuracy detection in low concentration analyte can hence be applied for control and prevention of hereditary diseases and understanding health effects of rare microbial strains.

bioengineering↗

bioRxiv2019

Metabolic Alterations in Human Peripheral Blood Mononuclear Cells Associate with Progression to Islet Autoimmunity and Type 1 Diabetes

Previous metabolomics studies suggest that type 1 diabetes (T1D) is preceded by specific metabolic disturbances. Here we asked whether distinct metabolic patterns occur in peripheral blood mononuclear cells (PBMCs) of children later developing pancreatic {beta}-cell autoimmunity or overt T1D. In a longitudinal cohort setting, PBMC metabolomic analysis was applied in children who either (1) progressed to T1D (PT1D, n=34), (2) seroconverted to [≥]1 islet autoantibody without progressing to T1D (P1Ab, n=27), or (3) remained autoantibody negative during follow-up (CTRL, n=10). During the first year of life, levels of most lipids and polar metabolites were lower in PT1D and P1Ab, versus CTRLs. Pathway overrepresentation analysis suggested alanine, aspartate, glutamate, glycerophospholipid and sphingolipid metabolism were overrepresented in PT1D. Genome-scale metabolic models of PBMCs in T1D progression were developed using available transcriptomics data and constrained with metabolomics data from our study. Metabolic modeling confirmed altered ceramide pathways as specifically associated with T1D progression.

molecular biology↗

bioRxiv2018

Persistent alterations in plasma lipid profiles prior to introduction of gluten in the diet associate with progression to celiac disease

Background and AimsCeliac disease (CD) is a chronic enteropathy characterized by an autoimmune reaction in the small intestine in genetically-susceptible individuals. Gluten is the required environmental trigger of clinical CD, but the underlying causes of the autoimmune reaction remain unknown. Herein, we apply lipidomics to elucidate the early events preceding clinical CD in a prospective study of children observed from birth until diagnosis of CD and subsequent introduction of a gluten-free diet.\n\nMethodsMass spectrometry-based lipidomics profiling was applied to a longitudinal series of 233 plasma samples from the Type 1 Diabetes Prediction and Prevention (DIPP) study, spanning the period between birth and the introduction of a gluten-free diet following CD diagnosis (n=23 CD progressors, n=23 controls matched for gender, HLA risk, period of birth, and age).\n\nResults23 children progressed to CD at a mean age of 4.8 years. They showed increased amounts of triacylglycerols (TGs) of low carbon number and double bond count and a decreased level of phosphatidylcholines by 3 months of age as compared to controls. These differences were exacerbated with age but were not observed at birth. No significant differences were observed in essential (dietary) TGs such as those containing polyunsaturated fatty acids.\n\nConclusionOur findings suggest that abnormal lipid metabolism associated with development of clinical CD may occur prior to the introduction of gluten to the diet. Moreover, our data suggest that the specific TGs found elevated in CD progressors may be due to a host response to compromised intake of essential lipids in the small intestine, requiring de novo lipogenesis.

systems biology↗

bioRxiv2018

3D micro-environment regulates NF-κβ dependent adhesion to induce monocyte differentiation

Differentiation of monocytes entails their relocation from blood to the tissue, hence accompanied by an altered physicochemical micro-environment. While the mechanism by which the biochemical make-up of the micro-environment induces differentiation is known, the fluid-like to gel-like transition in the physical micro-environment is not well understood. Monocytes maintain non-adherent state to prevent differentiation. We establish that irrespective of the chemical makeup, a 3D gel-like micro-environment induces a positive-feedback loop of adhesion-MAPK-NF-{kappa}{beta} activation to facilitate differentiation. In 2D fluid-like micro-environment, adhesion alone is capable of inducing differentiation via the same positive-feedback signalling. Chemical inducer treatment in fluid-like micro-environment, increases the propensity of monocyte adhesion via a brief pulse of p-MAPK. The adhesion subsequently elicit differentiation, establishing that adhesion is both necessary and sufficient to induce differentiation in 2D/3D micro-environment. Our findings challenge the notion that adhesion is a result of monocyte differentiation. Rather its the adhesion which triggers the differentiation of monocytes. MAPK, and NF-{kappa}{beta} being key molecules of multiple signaling pathways, we hypothesize that biochemically inert 3D gel-like micro-environment would also influence other cellular functions.\n\nSummary statementThis article brings out a new insight into the novel mechanisms of monocyte differentiation solely driven by physical micro-environment and adhesion.

cell biology↗