Biology subjects

Banerjee, S.

Publications and source records attributed to Banerjee, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Mapping DHPS Evolvability: Identification of Novel Evolutionarily Critical Sub-Structure through Evolutionary and Structural Analyses of DHPS

Protein evolution shapes pathogen adaptation-landscape, particularly in developing drug resistance. The rapid evolution of target proteins under antibiotic pressure leads to escape mutations leading to the problem of antibiotic resistance. A deep understanding of the evolutionary dynamics of antibiotic target proteins presents a plausible intervention strategy for disrupting the evolutionary trajectory of resistance. Mutations in Dihydropteroate synthase (DHPS), an essential folate pathway protein and a key target for sulfonamide antibiotics, result in reduced antibiotic binding, leading to resistance. Deploying an array of statistical analyses on the DHPS sequence-space and integrating those with deep mutational analysis and structure-based network-topology models we identified critical DHPS-subsequences. Our analysis of the frustration landscape of DHPS predicts how conformational and mutational changes shift the energy distributions within the DHPS substructures. Combining dimensionality reduction and optimality analysis we identified a substructure critical to DHPS evolvability, and computed its druggablity. Our integrated evolution and structure-informed framework identified a DHPS-substructure with significant evolutionary and structural impact. Targeting this region could constrain DHPS evolvability and disrupt the resistome, presenting a new avenue for antibiotic development and contributing to the broader effort to address the problem of antibiotic resistance.

biophysics↗

bioRxiv2024

Physical traits of supercompetitors in cell competition

Cell competition is a fitness control mechanism in tissues, where less fit cells are eliminated to maintain tissue homeostasis. Two primary mechanisms of cell elimination have been identified in cell competition studies: contact-dependent cell death and mechanical compression-driven apoptosis. While both occur in tissues, their combined impact on population dynamics is unclear. Here we develop a cell-based computational model to study competition between two cell types with differing physical properties. The model integrates cellular mechanics with cell-cycle dynamics, contact-induced apoptosis, and cell extrusion via mechanical stress. Using this model, we explored how differences in physical traits between cell types influence competitive interactions. Our findings show that differences in cell compressibility alone can drive mechanical competition, with stiffer cells outcompeting softer ones in otherwise identical populations. Surprisingly, mutations that reduce cell stiffness, combined with decreased contact inhibition of proliferation, can create a "soft" super-competitive mutant. We demonstrate that changes in apoptosis sensitivity, cell adhesion, and cell size significantly affect growth potential and susceptibility to apoptosis. Furthermore, mutant cell colonies require a critical colony size, dependent on cell compressibility, to overtake the surrounding wild-type tissue. For colonies below the critical size, the elimination process is stochastic, driven by a protrusive finger-like instability in the interface between two cells that promote invasion of the supercompetitors.

biophysics↗

bioRxiv2024

Patterns of leaf, flower and fruit phenology and environmental relationships in a seasonal tropical forest in the Indian Eastern Himalaya

Tree phenology plays an important role in determining the structure and function of tropical forest communities. However, there are few long-term studies on tree phenology from South Asia. We monitored 716 trees of 54 species monthly from 2011 to 2023 for leaf flush, flowering, and fruiting in Pakke Tiger Reserve, Arunachal Pradesh, India. We examined monthly patterns in the percentage of species and trees in leaf flush, flower and fruit and characterized phenological seasonality using circular statistics. Flowering periodicity was classified using Fourier analysis and we examined the relationships between phenological activity and temperature, rainfall, solar radiation and daylength using GAMLSS. Leaf flush and flowering were moderately seasonal, peaking in the warm dry season months of March to May. Fruiting patterns and their seasonality differed among dispersal modes. At the community level and for bird-dispersed species, fruiting was bimodal and relatively aseasonal, peaking in April and October. The highly seasonal fruiting of mammal-dispersed species peaked in October, while that of mechanically-dispersed species was bimodal and concentrated in the dry season months. The majority of species (78.13%) and trees (51.17%) flowered annually. Daylength, solar radiation and minimum temperature had significant nonlinear effects on phenology. This indicated the existence of narrow ranges of optimal climatic conditions for phenology, which could be affected by climate change. Our study emphasizes the need for long-term monitoring to rigorously quantify phenological patterns, particularly in the context of rapid global change.

plant biology↗

bioRxiv2024

DuReS: An R package for denoising experimental tandem mass spectrometry-based metabolomics data

Mass spectrometry-based untargeted metabolomics is a powerful technique for profiling small molecules in biological samples, yet accurate metabolite identification remains challenging. One of the primary obstacles in processing tandem mass spectrometry data is the prevalence of random noise peaks, which can result in false annotations and necessitate labor-intensive verification. A common method for removing noise from MS/MS spectra is intensity thresholding, where low-intensity peaks are discarded based on a user-defined cutoff or by analyzing the top "N" most intense peaks. However, determining an optimal threshold is often dataset-specific and may retain many noisy peaks. In this study, we hypothesize that true signal peaks consistently recur across replicate MS/MS spectra generated from the same precursor ion, unlike random noise. An optimal recurrence frequency of 0.12 (95% CI: 0.087-0.15) was derived using an open-source metabolomics dataset, which enhanced the dot product score between the experimental and library spectra by 66% post-denoising and resulted in a median signal and noise reduction of 5.83% and 99.07%, respectively. Validated across multiple metabolomics datasets, our denoising workflow significantly improved spectral matching metrics, leading to more accurate annotations and fewer false positives. Available freely as an R package, Denoising Using Replicate Spectra (DuReS) (https://github.com/BiosystemEngineeringLab-IITB/dures) is designed to remove noise while retaining diagnostically significant peaks efficiently. It accepts mzML files and feature lists from standard global untargeted metabolomics analysis software as input, enabling users to seamlessly integrate the denoising pipeline into their workflow without additional data manipulation.

bioinformatics↗

bioRxiv2024

Proliferation symmetry breaking in growing tissues

Morphogenesis of developing tissues results from anisotropic growth, typically driven by polarized patterns of gene expression. Here we propose an alternative model of anisotropic growth driven by self-organized feed-back between cell polarity, mechanical pressure, and cell division rates. Specifically, cell polarity alignment can induce spontaneous symmetry breaking in proliferation, resulting from the anisotropic distribution of mechanical pressure in the tissue. We show that proliferation anisotropy can be controlled by cellular elasticity, motility and contact inhibition, thereby elucidating the design principles for anisotropic morphogenesis.

biophysics↗

bioRxiv2024

Bibliometric Analysis of Circular RNA Cancer Vaccines and Their Emerging Impact

Circular RNA (circRNA) vaccines are emerging as a revolutionary strategy in cancer immunotherapy, offering novel mechanisms for inducing robust and durable immune responses. Unlike traditional linear mRNA vaccines, circRNAs exhibit exceptional stability, enhanced translational efficiency, and resistance to exonuclease degradation, making them ideal candidates for vaccine development. Recent studies have shown that circRNA vaccines play an important and specialized role in cancer treatment. However, there are currently no relevant bibliometric studies. This study aimed to apply bibliometrics and scientometrics to summarize the knowledge structure and research hotspots regarding the role of circRNA vaccines in cancer. Publications related to circRNA vaccines in cancer were searched on the Scopus database. VOSviewer and Scopus were used to conduct the analyses. This study summarizes the research trends and development of circRNA vaccines for cancer and also a comparative analysis between mRNA cancer vaccine and circRNA cancer vaccine identifying potential areas of focus, innovation and growth. This information will provide a reference for researchers to studying circRNA vaccines against cancer due to its increasing trends over recent times.

scientific communication and education↗

bioRxiv2024

Role of SCAL1 in Modulating Oxidative Stress, Cancer Stemness, Apoptotic Resistance in Tumorigenic Differentiation of Cigarette Smoke-Exposed BEAS-2B Cells

The smoke and cancer-associated lncRNA 1 (SCAL1) is an emergent biomarker in lung cancer. However, the precise role of SCAL1 as a mediator of tobacco smoke-induced lung carcinogenesis remains unclear. BEAS-2B cells were cultured and exposed to 20% cigarette smoke extract (CSE), followed by quantification of SCAL1. We evaluated the impact of SCAL1 on cell viability, ROS mitigation, cancer stemness, tumorigenic differentiation, cellular invasiveness, and apoptosis for different CSE incubation time points through SCAL1 expressional modulation using SCAL1-specific siRNAs and scrambled controls. We observed an upregulation of SCAL1 in cells exposed to CSE for 2, 4, and 6 hours, with the highest expression observed at 6 hours (p<0.001). Exposure of BEAS-2B cells to CSE showed the formation of focal adhesions and stress fibers resembling tunneling nanotubes. Intracellular ROS levels significantly increased upon CSE exposure compared to control cells (p<0.05). We found increased levels of anti-apoptotic and cancer stem (CSC) cell markers like BCL2, ALDH1A1, CD133, CD44, and TCTP and decreased levels of TP53 in CSE-exposed cells. Knockdown of SCAL1 using siRNA transfection reversed these effects at all time points. Additionally, we observed a significant decrease in the number of spheroid colonies in siSCAL1 (+) cells compared to siSCAL1 (-) cells (p<0.01) exposed to CSE. SCAL1 is pivotal in mediating cellular responses to cigarette smoke, leading to tumorigenic differentiation of BEAS-2B cells. Understanding the mechanisms could provide valuable insights into lung cancer pathogenesis and therapeutic approaches.

cancer biology↗

bioRxiv2024

The RNA binding ubiquitination ligase MEX3B regulates bFGF-dependent neuronal proliferation.

BackgroundE3 ubiquitin ligases, integral components of the proteasomal degradation cascade, are critical for regulating the cellular proteome via canonical proteasome-mediated protein degradation; however, the non-canonical functions of these ligases in neuronal development are poorly understood. Our study focuses on a special class of E3 ubiquitin ligases known as RNA Binding Ubiquitin Ligases (RBUL) that harbour RNA-binding domains; allowing them to acquire all the properties of RNA-binding proteins (RBPs) and regulate transcriptional or post-transcriptional changes associated with the control of gene expression in cellular phenotypes. We aim to identify one such RUBL in the context of the highly dynamic yet stringently controlled process of neural proliferation and neural fate determination. ResultsMEX3B protein is a member of the MEX3 family and a part of the RBUL class of E3 ligases. It is differentially expressed in Neural Progenitor Cells (NPCs) upon differentiation. Mex3b RNA and protein were found to have temporally opposing expression patterns in presence of basic fibroblast growth factor (bFGF), a key signalling protein involved in neuronal proliferation. MEX3B is required for maintenance of the proliferative state of NPCs, whereas, its knockdown promotes transition from proliferative to differentiation state even in presence of bFGF that restricts differentiation. Furthermore, the knockdown of MEX3B protein results in the appearance of morphological hallmarks associated with early stages of neuronal differentiation including increase in neurite length and complexity. MEX3B interacts with the pro-proliferative transcription activator REST and the long non-coding RNA, HOTAIR. The study suggests the existence of a bFGF-dependent, combinatorial axis involving Mex3b, REST and HOTAIR, for the maintenance of NPC proliferative states. ConclusionMEX3B, containing RNA binding motifs, is a unique E3 ligase that is necessary for bFGF-dependent proliferation. Mex3b protein invokes its non-canonical function of an RNA binding protein to form a tripartite complex with the transcription activator REST and HOTAIR lncRNA to define the proliferative state of NPCs. The study highlights a unique feature of special E3 ligases in neuronal proliferation during brain development that was previously overlooked.

neuroscience↗

bioRxiv2024

High throughput cell mechanotyping of cell response to cytoskeletal modulations using a microfluidic cell deformation system

Cellular mechanical properties influence cellular functions across pathological and physiological systems. The observation of these mechanical properties is limited in part by methods with a low throughput of acquisition or with low accessibility. To overcome these limitations, we have designed, developed, validated, and optimized a microfluidic cellular deformation system (MCDS) capable of mechanotyping suspended cells on a population level at a high throughput rate of [~]300 cells pers second. The MCDS provides researchers with a viable method for efficiently quantifying cellular mechanical properties towards defining prognostic implications of mechanical changes in pathology or screening drugs to modulate cytoskeletal integrity.

bioengineering↗

bioRxiv2024

The stage-specific regulation imposed by Importin beta-1 on HIV-1 propagation and infectivity dynamics

Dynamics of intra-host molecular evolution of viruses depend on the complexities of the cellular environments through which they transit. HIV infects several cell types in an infected human host, especially during chronic stages, which impose differential regulations on HIV persistence, driving it to latency, rapid propagation, or abortive infection. We observed that HIV-1 emerging from different cell-types differ in their encapsidated protein cargo, and infectivity. We investigated the role of Importin{beta}-1, which is encapsidated in virus emerging from CD4+T lymphocytes, but not in viruses from astrocytes. We deciphered that Importin{beta}-1 is packaged via interactions with HIV-1 Gag/Capsid. The encapsidated Importin{beta}-1 assisted nuclear-entry of the viral core and enhanced the infectivity during pre-integration stages. Conversely, high levels of endogenous Importin{beta}-1, which was observed to be induced upon infection and inflammatory stimulations, such as, IFNg/LPS treatments, restricted LTR-driven viral transcription during post-integration. The regulatory impact of Importin{beta}-1 was verified using primary CD4+T lymphocytes, thereby validating a non-canonical and novel role of Importin{beta}-1 as a restriction factor for HIV-1. Using deletion mutants, we demonstrate that the N-terminal domain of Importin{beta}-1 regulated viral transcription via SP1, and NRE regions of LTR. We propose that sequestering of Importin{beta}-1 by packaging in emerging virions thereby reducing its antiviral impact, is an adaptive strategy of a pathogen, supporting the concepts of evolutionary conflicts between viruses and hosts.

molecular biology↗

bioRxiv2024

Opioid Modulation of Differential Gene Expression and Neuronal Differentiation in the Ventricular-Subventricular Zone of Adult Male Zebra Finches

1The endogenous opioid system modulates diverse functions including pain, physiological functions and motivation. We had earlier demonstrated an increase in cell proliferation in the neurogenic niche of adult male zebra finches, following administration of the general opioid antagonist, naloxone. Since the mechanisms underlying opioid modulation of neurogenesis are poorly understood, we have investigated the molecular mechanisms underlying cell proliferation differentiation induced by the opioid system. Systemic naloxone or vehicle administration in adult male birds was followed by a whole transcriptome microarray assay of the ventricular-subventricular zone (V-SVZ). The analysis revealed 26 differentially expressed transcripts (expression fold change [≥] 1.5), encoding genes important for neuronal functions. The transcriptomics analysis using microarray identified a significant increase in the expression of precursor miRNA tgu-mir-124-201 transcript following inhibition of opioid receptors by naloxone. Our results suggested that the administration of naloxone triggers an increase in the expression of the pro-differentiating microRNA, miR-124, in the brains of adult zebra finches. Using quantitative real-time PCR, we found that the expression of miR-124-3p was higher in the V-SVZ of naloxone-treated versus control birds. Furthermore, the density of neuroblasts was higher in the ventral V-SVZ adjacent to the striatal nucleus Area X, but not in the V-SVZ above the pallial nucleus, HVC, both of which are involved in singing. Since miR-124 targets signalling pathways important for neuronal proliferation and differentiation, our findings suggest that microRNA-124 may be involved in the increase in neurogenesis in adult songbirds induced by altering opioid modulation.

neuroscience↗

bioRxiv2024

Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening

Nuclear condensates play many important roles in chromatin functions, but how cells regulate their nucleation and growth within the complex nuclear environment is not well understood. Here, we report how condensate properties and chromatin mechanics dictate condensate growth dynamics in the nucleus. We induced condensates with distinct properties using different proteins in human cell nuclei and monitored their growth. We revealed two key physical mechanisms that underlie droplet growth: diffusion-driven or ripening-dominated growth. To explain the experimental observations, we developed a quantitative theory that uncovers the mechanical role of chromatin and condensate material properties in regulating condensate growth in a heterogeneous environment. By fitting our theory to experimental data, we find that condensate surface tension is critical in determining whether condensates undergo elastic or Ostwald ripening. Our model also predicts that chromatin heterogeneity can influence condensate nucleation and growth, which we validated by experimentally perturbing the chromatin organization and controlling condensate nucleation. By combining quantitative experimentation with theoretical modeling, our work elucidates how condensate surface tension and chromatin heterogeneity govern nuclear condensate ripening, implying that cells can control both condensate properties and the chromatin organization to regulate condensate growth in the nucleus.

biophysics↗

bioRxiv2024

An Introductory Implementation of Breast Cancer Detection from Mammograms and Pixel Intensity with Efficient-Net Other Neural Nets

In the world of civilized medical scientific progression, cancer has become a very serious threat for the natural survival of human beings where breast cancer stays to be the second most dangerous type. Mostly women are embracing very pathetic death because of the delayed detection of the cancer cell in the certain period of their life. Machine Learning mechanism can definitely help at the stage of medical imaging which can escalate the diagnosis of the cancer cells at a very early age of its biological formation and development. We focused upon the deep learning approach to classify the normal and abnormal breast according to the medical imaging from the MIAS dataset of Mammograms and Pixel Intensity. The Convolution Neural Network (CNN) alongside ResNet, AmoebaNet and EfficientNet have been used for the detection with 330 mammograms in which 194 images are normal and 136 are having the identification of abnormal breasts. The accuracy of the entire experimental results was carrying the torch of potential legacy of deep learning in the medical imaging arena. The research is ongoing for the further development and optimization of CNN, AmoebaNet-C and EfficientNet architecture for the Pixel Intensity with higher accuracy, proper segmentation and masking. Source code of this research is available here: https://github.com/ac005sheekar/Breast-Cancer-Detection-with-Pixel-Intensity/

bioinformatics↗

bioRxiv2024

Endothelial ERG programs neutrophil transcriptome for sustained anti-inflammatory vascular niche

Neutrophils (PMNs) reside as a marginated pool within the vasculature, ready for deployment during infection. However, how endothelial cells (ECs) control PMN extravasation and activation to strengthen tissue homeostasis remains ill-defined. Here, we found that the vascular ETS-related gene (ERG) is a generalized mechanism regulating PMN activity in preclinical tissue injury models and human patients. We show that ERG loss in ECs rewired PMN-transcriptome, enriched for genes associated with the CXCR2-CXCR4 signaling. Rewired PMNs compromise mice survival after pneumonia and induced lung vascular inflammatory injury following adoptive transfer into naive mice, indicating their longevity and inflammatory activity memory. Mechanistically, EC-ERG restricted PMN extravasation and activation by upregulating the deubiquitinase A20 and downregulating the NF{kappa}B-IL8 cascade. Rescuing A20 in EC-Erg-/- endothelium or suppressing PMN-CXCR2 signaling rescued EC control of PMN activation. Findings deepen our understanding of EC control of PMN-mediated inflammation, offering potential avenues for targeting various inflammatory diseases. HighlightsO_LIERG regulates trans-endothelial neutrophil (PMN) extravasation, retention, and activation C_LIO_LILoss of endothelial (EC) ERG rewires PMN-transcriptome C_LIO_LIAdopted transfer of rewired PMNs causes inflammation in a naive mouse C_LIO_LIERG transcribes A20 and suppresses CXCR2 function to inactivate PMNs C_LI In brief/blurbThe authors investigated how vascular endothelial cells (EC) control polymorphonuclear neutrophil (PMN) extravasation, retention, and activation to strengthen tissue homeostasis. They showed that EC-ERG controls PMN transcriptome into an anti-adhesive and anti-inflammatory lineage by synthesizing A20 and suppressing PMNs-CXCR2 signaling, defining EC-ERG as a target for preventing neutrophilic inflammatory injury.

immunology↗

bioRxiv2024

RV-specific Targeting of Snai1 Rescues Pulmonary Hypertension-induced Right Ventricular Failure by Inhibiting EndMT and Fibrosis via LOXL2 Mediated Mechanism

BackgroundPulmonary hypertension (PH)-induced right ventricular (RV) failure (PH-RVF) is a significant prognostic determinant of mortality and is characterized by RV hypertrophy, endothelial-to-mesenchymal transition (EndMT), fibroblast-to-myofibroblast transition (FMT), fibrosis, and extracellular matrix (ECM)-remodeling. Despite the importance of RV function in PH, the mechanistic details of PH-RVF, especially the regulatory control of RV EndMT, FMT, and fibrosis, remain unclear. The action of transcription factor Snai1 is shown to be mediated through LOXL2 recruitment, and their co-translocation to the nucleus, during EndMT progression. We hypothesize that RV EndMT and fibrosis in PH-RVF are governed by the TGF{beta}1-Snai1-LOXL2 axis. Furthermore, targeting Snai1 could serve as a novel therapeutic strategy for PH-RVF. MethodsAdult male Sprague Dawley rats (250-300g) received either a single subcutaneous injection of Monocrotaline (MCT, 60mg/kg, n=9; followed for 30-days) or Sugen (SU5416 20mg/kg, n=9; 10% O2 hypoxia for 3-weeks followed by normoxia for 2-weeks) or PBS (CTRL, n=9). We performed secondary bioinformatics analysis on the RV bulk RNA-Seq data from MCT, SuHx, and PAB rats and human PH-PVF. We validated EndMT and FMT and their association with Snai1 and LOXL2 in the RVs of MCT and SuHx rat models and human PH-RVF using immunofluorescence, qPCR, and Western blots. For in vivo Snai1 knockdown (Snai1-KD), MCT-rats either received Snai1-siRNA (n=7; 5nM/injection every 3-4 days; 4-injections) or scramble (SCRM-KD; n=7) through tail vein from day 14-30 after MCT. Echocardiography and catheterization were performed terminally. Bulk RNASeq and differential expression analysis were performed on Snai1- and SCRM-KD rat RVs. In vitro Snai1-KD was performed on human coronary artery endothelial cells (HCAECs) and human cardiac fibroblasts (HCFs) under hypoxia+TGF{beta}1 for 72-hrs. ResultsPH-RVF had increased RVSP and Fulton index and decreased RV fractional area change (RVFAC %). RV RNASeq demonstrated EndMT as the common top-upregulated pathway between rat (MCT, SuHx, and PAB) and human PH-RVF. Immunofluorescence using EndMT- and FMT-specific markers demonstrated increased EndMT and FMT in RV of MCT and SuHx rats and PH-RVF patients. Further, RV expression of TGF{beta}1, Snai1, and LOXL2 was increased in MCT and SuHx. Nuclear co-localization and increased immunoreactivity, transcript, and protein levels of Snai1 and LOXL2 were observed in MCT and SuHx rats and human RVs. MCT rats treated with Snai1-siRNA demonstrated decreased Snai1 expression, RVSP, Fulton index, and increased RVFAC. Snai1-KD resulted in decreased RV-EndMT, FMT, and fibrosis via a LOXL2-dependent manner. Further, Snai1-KD inhibited hypoxia+TGF{beta}1-induced EndMT in HCAECs and FMT in HCFs in vitro by decreasing perinuclear/nuclear Snai1+LOXL2 expression and co-localization. ConclusionsRV-specific targeting of Snai1 rescues PH-RVF by inhibiting EndMT and Fibrosis via a LOXL2-mediated mechanism.

physiology↗

bioRxiv2024

Experimental type 1 diabetes metabolically rejuvenates CD8+ T cells for improved control of tumor growth through an IGF1-IGF1R axis

AbstractEpidemiological studies suggest that patients with pre-existing type 1 diabetes (T1D) have a decreased risk of developing melanoma, prostate cancer, and breast cancer, although the underlying mechanism remains to be elucidated. In translational modelling, we observed that streptozotocin (STZ) induced T1D mice exhibited restricted melanoma and carcinoma (mammary, lung and colon) growth in association with extended overall survival. Tumor-infiltrating CD8+ T cells were found to be responsible for tumor growth restriction. Tumor infiltrating CD8+ T cells but not tumor cells themselves exhibited higher glycolytic and cytotoxic activities in T1D hosts. Such improved anti-tumor T cell function was linked to selective upregulated expression of insulin-like growth factor 1, insulin-like growth factor 1 receptor, and phospho-mTOR in CD8+ T cells in the TME. T1D patient derived CD8+ T cells displayed superior activation in vitro after tumor antigen stimulation vs. non-diabetic CD8+ T cells. Activation of T1D patient derived CD8+ T cells was sensitive to targeted antagonism of IGF1R and mTOR, supporting the operational involvement of the IGF1R-mTOR signaling axis. Our results suggest that selective activation of the intrinsic IGF1R-mTOR signaling axis in CD8+ T cells represents a preferred endpoint to achieving more effective immunotherapy outcomes and improved cancer patient management. SignificanceExperimental type 1 diabetes decelerates tumor growth through metabolic activation of cytotoxic T cells dependent on an IGF1R-mTOR signaling pathway. CD8+IGF1R+IGF1+ T cells play a crucial role in T1D dependent tumor control.

cancer biology↗

bioRxiv2024

Unusual lineage plasticity revealed by YY1 knockout in pro-B cells

During B cell development, cells progress through multiple developmental stages with the pro-B cell stage defining commitment to the B cell lineage. YY1 is a ubiquitous transcription factor that is capable of both activation and repression functions. We find here that knockout of YY1 at the pro-B cell stage eliminates B lineage commitment. YY1 knockout pro-B cells can generate T lineage cells in vitro using the OP9- DL4 feeder system, as well as in vivo after injection into sub-lethally irradiated Rag1-/- mice. These T lineage-like cells lose their B lineage transcript profile and gain a T cell lineage profile. Single cell-RNA-seq experiments showed that as YY1 knockout pro-B cells transition into T lineage cells, various cell clusters adopt transcript profiles representing a multiplicity of hematopoietic lineages indicating unusual lineage plasticity. Given the ubiquitous nature of YY1 and its dual activation and repression functions, YY1 likely regulates commitment in multiple cell lineages.

developmental biology↗

bioRxiv2024

Heterotypic Seeding Generates Mixed Amyloid Polymorphs

Aggregation of the amyloid {beta} (A{beta}) peptide into fibrils represents one of the major biochemical pathways underlying the development of Alzheimers disease (AD). Extensive studies have been carried out to understand the role of fibrillar seeds on the overall kinetics of amyloid aggregation. However, the precise effect of seeds that are structurally or sequentially different from A{beta} on the structure of the resulting amyloid aggregates is yet to be fully understood. In this work, we use nanoscale infrared spectroscopy to probe the spectral facets of individual aggregates formed by aggregating A{beta}42 with antiparallel fibrillar seeds of A{beta} (16-22) and E22Q A{beta} (1-40) Dutch mutant and demonstrate that A{beta} can form heterotypic or mixed polymorphs that deviate significantly from its expected parallel cross {beta} structure. We further show that formation of heterotypic aggregates is not limited to coaggregation of A{beta} and its isomers, and that the former can form heterotypic fibrils with alpha synuclein and brain protein lysates. These findings highlight the complexity of A{beta} aggregation in AD and underscore the need to explore how A{beta} interacts with other brain components, which is crucial for developing better therapeutic strategies for AD.

biophysics↗