Biology subjects

Chakraborty, N.

Publications and source records attributed to Chakraborty, N..

4 recordsLinked to original sources

bioRxiv2022

Multispecies autocatalytic RNA reaction networks in coacervates

Robust and dynamic localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of an RNA system within charge-rich coacervates where catalytic RNAs are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates -- both in micron sized droplets as well as a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, these collectively autocatalytic reaction networks endow unique compositional identities to the coacervates which in turn transiently protect the identity against external perturbations, due to differential molecular transport and reaction rates. Our results establish a compartmentalised chemical system possessing a compositional identity possessing a balance between robustness and variability required for chemical evolution.

evolutionary biology↗

bioRxiv2022

FH variant pathogenicity promotes purine salvage pathway dependence in kidney cancer

The tricarboxylic citric acid cycle enzyme fumarate hydratase (FH) is a tumor suppressor. When lost in cells, its substrate fumarate accumulates to mM levels and drives oncogenic signaling and transformation. Germline alterations lead to an autosomal dominant condition known as hereditary leiomyomatosis and renal cell cancer (HLRCC) where patients are predisposed to various benign tumors and an aggressive form of kidney cancer. FH alterations of unclear significance are frequently observed with germline testing; thus, there is an unmet need to classify FH variants by their cancer-associated risk, allowing for screening, early diagnosis and treatment. Here we quantify catalytic efficiency of 74 FH variants of uncertain significance. Over half were enzymatically inactive which is strong evidence of pathogenicity. We generated a panel of HLRCC cell lines expressing FH variants with a range of catalytic activities, then correlated fumarate levels with metabolic features. We found that fumarate accumulation blocks purine biosynthesis, rendering FH-deficient cells reliant on purine salvage to maintain purine nucleotide pools. Genetic or pharmacologic inhibition of the purine salvage pathway reduced HLRCC tumor growth in vivo. Together, these findings suggest pathogenicity of many patient-associated FH variants and reveal purine salvage as a targetable vulnerability in FH-deficient tumors. Statement of SignificanceThis study functionally characterizes patient-associated FH variants with unknown significance for pathogenicity. This study also reveals nucleotide salvage pathways as a targetable feature of FH-deficient cancers, which are shown to be sensitive to the purine salvage pathway inhibitor 6-mercaptopurine. This presents a new rapidly translatable treatment strategy for FH-deficient cancers.

cancer biology↗

bioRxiv2022

Computational multiphase characterization of perfusion trends inside biomimetic reduced-order dense tumors

Dense fibrous extracellular constitution of solid tumors exerts high resistance to diffusive transport into it; additionally, the scarcity of blood and lymphatic flows hinders convection. The complexity of fluidic transport mechanisms in such tumor environments still presents open questions with translational end goals. For example, clinical diagnosis and targeted drug delivery platforms for such dense tumors can ideally benefit from a quantitative framework on plasma uptake into the tumor. In this study, we present a computational model for physical parameters that may influence blood percolation and penetration into a simple biomimetic solid tumor geometry. The model implements 3-phase viscous laminar transient simulation to mimic the transport physics inside a tumor-adhering blood vessel and measures the constituent volume fractions of the three considered phases, viz. plasma, RBCs (Red Blood Cells, also known as "erythrocytes"), and WBCs (White Blood Cells, also known as "leukocytes") at three different flow times, while simultaneously recording the plasma pressure and velocity at the entry point to the tumors extracellular space. Subsequently, to quantify plasma perfusion within the tumor zone, we have proposed a reduced-order 2D transport model for the tumor entry zone and its extracellular space for three different fenestra diameters: 0.1, 0.3, and 0.5 m; the simulations were 2-phase viscous laminar transient. The findings support the hypothesis that plasma percolation into the tumor is proportional to the leakiness modulated by the fenestra openings, quantifiable through the opening sizes.

biophysics↗

bioRxiv2019

Active modulation of Hydrogen bonding by sericin enhances cryopreservation outcomes

Cryopreservation of cells without any toxicity concerns is a critical step in ensuring successful clinical translation of cell-based technologies. Mitigating the toxicity concerns related to most of the commonly used cryoprotectants including dimethyl sulfoxide (DMSO) is an active area of research in cryobiology. In recent years use of additives including polymeric proteins such has sericin have been explored as an additive to cryoprotectant formulations. In this study the thermophysical effect of addition of sericin was investigated. The effect of presence of sericin on the H-bonding strength was investigated using Raman microspectroscopy and other thermophysical effects were quantified using differential scanning calorimetry (DSC) techniques. Finally, the prospect of using sericin as an additive to cryoprotectant formulation was investigated by monitoring cellular viability and growth following exposure to cryogenic temperatures in hepatocellular carcinoma cells. Results indicate significant improvement in post-thaw viability when sericin is used as an additive to DMSO based formulations. While use of trehalose as an additive has beneficial effects by itself, combined usage of sericin and trehalose as additives did result in an improved overall long-term growth potential of the cells.\n\nStatement of SignificanceThis study provides for powerful biophysical understanding of how sericin can be used as an additive for cryoprotectant solutions, which allows storage of biologics at low temperatures. It is desirable to replace current components of cryoprotectant formulation (such as DMSO) due to innate toxicity and metabolic derangements to cells. The ability of sericin to improve cryoprotective solutions was mechanistically characterized by Raman microspectroscopy, which allows for molecular level characterization of the nature of H-bonding in aqueous environments in presence of solution components. Thermodynamic analysis of the cryoprotectant solutions containing sericin was undertaken to quantify the relation between solution composition and cryopreservation outcome. This analytical study provides a basis for designing better cryoprotectants with lower thermophysical injury and higher cellular yields.

bioengineering↗