Biology subjects

Chatterjee, T.

Publications and source records attributed to Chatterjee, T..

12 recordsLinked to original sources

bioRxiv2026

PINPOINT enables non-destructive nanoscopic quality control of individual lipid nanoparticles and their mRNA cargo

Quality control of lipid nanoparticles (LNPs) is central to development of mRNA therapeutics, yet ensemble measurements obscure critical heterogeneity in particle morphology and mRNA cargo loading. Here we introduce PINPOINT (Profiling Individual Nanoparticles with Precise Observation of INternalized Therapeutics), a single-particle nanoscopy platform for non-destructive, multiparametric profiling of preformulated LNP samples. Super-resolution imaging with Nile Red resolves size and morphology, while an optimized permeabilization strategy provides selective access to encapsulated mRNA without compromising LNP integrity. Single-particle fluorescence measurements, including RiboGreen and sequence-specific probes, enable quantification and validation of mRNA loading and identity. Comparative analyses of bare and encapsulated mRNA reveal kinetic and structural features, exposing heterogeneity masked by bulk assays. By integrating structural and molecular readouts at the single-particle level, PINPOINT establishes a quantitative framework for assessing of LNP composition and payload distribution, offering actionable insights for improving batch consistency and guiding the rational design of next-generation mRNA delivery systems.

biophysics↗

bioRxiv2026

Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley

Wastewater sequencing using probe-capture enrichment of public health-relevant viruses is a powerful, non-intrusive approach to monitor infectious diseases, but performance depends on sample type and processing approach. We compared two processing pipelines from wastewater influent samples collected at three timepoints across three wastewater treatment facilities. Each sample was split for parallel processing, with viruses concentrated (1) directly from whole influent using nano-sized affinity particles and (2) by settling and dewatering the solids fraction. Combined DNA/RNA extracts were prepared into libraries using a pre-commercial Illumina protocol, then probe-capture enrichment was performed with Illumina Viral Surveillance Panel (VSP) v1 (66 targets) and v2 (242 targets). Sequencing depth was increased for VSP v2 to accommodate the expanded target set. On average, 160 +/- 146 viral species were detected per sample, with wastewater fraction (sample type) explaining 19% of the variance in viral abundances. Solids contained a higher abundance of DNA viruses compared to RNA viruses, while influent exhibited the inverse. Metagenomic analysis of the VSP v2 sequencing data detected more viral species in influent (median 358) than in solids (median 184), but probe-capture enrichment produced more comparable target-virus readouts across fractions, supporting the use of either fraction for wastewater-based epidemiology.

genomics↗

bioRxiv2025

KDM5B expression is suppressed by MYC in a negative feedback loop to promote cell survival.

Both c-MYC and KDM5B are global regulators of gene transcription, cell identity, and master transcription factors in hematopoietic malignancies. In this study we link these two critical factors in a negative feedback loop that controls apoptosis and cell survival. We find the MYC specifically downregulates KDM5B, thereby inhibiting its transcriptional repressive functions. Loss of KDM5B abrogates the cell death response to MYC withdrawal in MYC-dependent cells, indicating KDM5B mediates cell death. We find that KDM5B regulates the MYC network, and specifically demethylates the MYC locus. In summary we have discovered a negative feedback loop between MYC and KDM5B. The MYC-dependent suppression of KDM5B leads to a global increase in H3K4me3 methylation, transcriptional activity, and increase cell survival and tumor progression.

cancer biology↗

bioRxiv2025

Myeloid FtH Regulates Macrophage Response to Kidney Injury by Modulating Snca and Ferroptosis

This study explored the role of myeloid ferritin heavy chain (FtH) in coordinating kidney iron trafficking in health and disease. Synuclein- (Snca) was the sole iron-binding protein upregulated in response to myeloid FtH deletion (FtH{Delta}/{Delta}). Following kidney injury, FtH{Delta}/{Delta} mice showed worsened kidney function. Transcriptome analysis revealed coupling of FtH deficiency with ferroptosis activation, a regulated cell death associated with iron accumulation. Adverse effects of ferroptosis were evidenced by upregulation of ferroptosis-related genes, increased oxidative stress markers, and significant iron deposition in kidney tissues. This iron buildup in FtH{Delta}/{Delta} kidneys stemmed from macrophage reprogramming into an iron-recycling phenotype, driven by Spic induction. Mechanistically, we establish that monomeric Snca functions as a ferrireductase catalyst, intensifying oxidative stress and triggering ferroptosis. Additionally, Snca accumulates in kidney diseases distinguished by leukocyte expansion across species. These findings position myeloid FtH as a pivotal orchestrator of the FtH-Snca-Spic axis driving macrophage reprogramming and kidney injury. HighlightsO_LIMyeloid FtH deficiency drives kidney injury via activation of ferroptosis C_LIO_LIM{Phi} FtH deficiency induces Snca, linking iron dysregulation to M{Phi} function and response to kidney injury C_LIO_LIFerrireductase activity of monomeric Snca augments oxidative stress, promoting lipid peroxidation and ferroptosis C_LI In briefM{Phi} FtH modulates Snca and Spic to coordinate the injury response, linking iron trafficking to ferroptosis-induced kidney injury

pathology↗

bioRxiv2025

A unifying model for microRNA-guided silencing of messenger RNAs

Silencing by the miRNA-guided RNA induced silencing complex (miRISC) is dependent on Ago2-chaperoned base pairing between the miRNA 5' seed (5'S) and a complementary sequence in the 3' untranslated region of an mRNA. Prevailing mechanistic understanding posits that initial 5'S pairing can further allow functional base pair expansion into the 3' non-seed (3'NS), while functionally distinct non-canonical pairing was reported between only the 3'NS and the mRNA coding sequence. We developed single-molecule kinetics through equilibrium Poisson sampling (SiMKEPS) to measure highly precise binding and dissociation rate constants of varying-length target sequences to 5'S and 3'NS in a paradigmatic miRISC isolated from human cells, revealing distinct stable states of miRISC with mutually exclusive 5'S and 3'NS pairing. Our data suggest conformational rearrangements of the Ago2-bound miRNA that regulate alternative 5'S-and 3'NS-driven target recognition. The resulting model reconciles previously disparate observations and deepens our acumen for successfully marshaling RNA silencing therapies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/643529v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1e92bb5org.highwire.dtl.DTLVardef@1348249org.highwire.dtl.DTLVardef@559fdborg.highwire.dtl.DTLVardef@1721b74_HPS_FORMAT_FIGEXP M_FIG C_FIG In brief: In this study, Chatterjee et al. developed a technique to characterize and identify multiple conformations of the RNA-induced silencing complex (RISC) present in human cells. Two distinct pathways of target recognition through different RISC conformations reconcile previously observed divergent findings on the microRNA (miRNA) binding mechanism to messenger RNA (mRNA). HighlightsO_LISiMKEPS is developed to precisely measure binding and dissociation of miRISC:mRNA C_LIO_LISingle human miRISC molecules exhibit mutually exclusive seed and non-seed pairing C_LIO_LISiMKEPS unveils conformational changes of single miRNAs bound to Ago2 C_LIO_LIResulting model reconciles previously divergent findings, supporting RNAi therapies C_LI

biophysics↗

bioRxiv2025

Chromato-kinetic fingerprinting enables multiomic digital counting of single disease biomarker molecules

Early and personalized intervention in complex diseases requires robust molecular diagnostics, yet the simultaneous detection of diverse biomarkers--microRNAs (miRNAs), mutant DNAs, and proteins--remains challenging due to low abundance and preprocessing incompatibilities. We present Biomarker Single-molecule Chromato-kinetic multi-Omics Profiling and Enumeration (Bio-SCOPE), a next-generation, triple-modality, multiplexed detection platform that integrates both chromatic and kinetic fingerprinting for molecular profiling through digital encoding. Bio-SCOPE achieves femtomolar sensitivity, single-base mismatch specificity, and minimal matrix interference, enabling precise, parallel quantification of up to six biomarkers in a single sample with single-molecule resolution. We demonstrate its versatility in accurately detecting low-abundance miRNA signatures from human tissues, identifying upregulated miRNAs in the plasma of prostate cancer patients, and measuring elevated interleukin-6 (IL-6) and hsa-miR-21 levels in cytokine release syndrome patients. By seamlessly integrating multiomic biomarker panels on a unified, high-precision platform, Bio-SCOPE provides a transformative tool for molecular diagnostics and precision medicine.

biophysics↗

bioRxiv2025

Following the Robot's Lead: Predicting Human and Robot Movement from EEG in a Motor Learning HRI Task

Human-robot interaction (HRI) offers unique opportunities to study the neuroscience of human motor control through controlled and reproducible sensory stimuli. In this study, we introduce an innovative neuroscience-HRI framework inspired by the Serial Reaction Time (SRT) task, that combines EEG with a task where a humanoid robot performs preprogrammed movement sequences that are mirrored by a human participant in real time. The use of a humanoid robot ensures precise and repeatable sensory-motor stimuli in the 3D peripersonal space of the participant, providing experimental conditions that may be challenging to replicate with traditional methods. Behavioral performance is assessed by measuring the temporal lag between human and robot movements, which decreases with training, reflecting motor sequence learning. Concurrently, EEG data from the human participant is analyzed to reveal neural correlates of learning and movement dynamics. Event-Related Spectral Perturbations (ERSP) in theta, mu, and beta frequency bands demonstrate distinct patterns associated with rest, fixation, and movement. Furthermore, the ERSP changes over successive trials reflect the progression of sequence learning, highlighting the relationship between neural oscillations and motor learning. A Markov-Switching Linear Regression model further decodes EEG signals to predict movement parameters including both human and robot position and velocity in a time-resolved manner. Our findings highlight the potential of HRI as a robust platform for neuroscience research and underscore the value of EEG-based neural decoding in understanding motor sequence learning. This work suggests further advances for integrating robotics into neuroscience and rehabilitation research.

neuroscience↗

bioRxiv2024

Single-cell genomics and regulatory networks for 388 human brains

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2022

An antibody-drug conjugate targeting GPR56 demonstrates efficacy in preclinical models of colorectal cancer

Antibody-drug conjugates (ADCs) have become an increasingly successful class of anticancer therapy, particularly within the past few years. Though ADCs are in clinical trials for colorectal cancer (CRC), a candidate has yet to be approved. CRC continues to be a leading cause of cancer-related death, emphasizing the need to identify novel target antigens for ADC development. GPR56, a member of the 7TM receptor family, is upregulated in colorectal tumors compared to normal tissues and located on the surface of CRC cells, making it a promising ADC target. Furthermore, high GPR56 expression occurs in tumors that are microsatellite stable, negative for the CpG methylator phenotype, and show chromosomal instability. We previously reported the generation of a high affinity GPR56-specific monoclonal antibody, 10C7, and we have now mapped the epitope to the C-terminal end of the extracellular domain, proximal to the GPCR proteolysis site. Here, we describe the development of a duocarmycin-conjugated 10C7 ADC. 10C7 co-internalized with GPR56 and trafficked to the lysosomes of CRC cells, which is critical for efficient ADC payload release. Evaluation of the ADC in a panel of CRC cell lines and tumor organoids with different levels of GPR56 expression showed the ADC selectively induced cytotoxicity at low nanomolar concentrations in a GPR56-dependent manner. A nontargeting control ADC showed minimal to no activity. Furthermore, GPR56 ADC exhibited significant antitumor efficacy against GPR56-expressing patient-derived xenograft models of CRC. This study provides rationale for the development of a GPR56-targeted ADC approach to potentially treat a large fraction of CRC patients.

cancer biology↗

bioRxiv2021

A Robust, Low-Cost Instrument for Real-time Colorimetric Isothermal Nucleic Acid Amplification

The COVID-19 pandemic has highlighted the need for broader access to molecular diagnostics. Colorimetric isothermal nucleic acid amplification assays enable simplified instrumentation over more conventional PCR diagnostic assays and, as such, represent a promising approach for addressing this need. In particular, colorimetric LAMP (loop-mediated isothermal amplification) has received a great deal of interest recently. However, there do not currently exist robust instruments for performing these kinds of assays in high throughput with real-time readout of amplification signals. To address this need, we developed LARI, the LAMP Assay Reader Instrument. We have deployed over 50 LARIs for routine use in R&D and production environments, with over 12,000 assays run to date. In this paper, we present the design and construction of LARI along with thermal, optical, and assay performance characteristics. LARI can be produced for under $1500 and has broad applications in R&D, point-of-care diagnostics, and global health.

bioengineering↗

bioRxiv2021

Redox Nanomedicine Cures Chronic Kidney Disease (CKD) by Mitochondrial Reconditioning

Targeting reactive oxygen species (ROS) while maintaining cellular redox signaling is crucial in the development of redox medicine for the therapeutic benefit as the origin of several prevailing diseases including chronic kidney disease (CKD) is linked to ROS imbalance and associated mitochondrial dysfunction. Here, we have shown that an indigenously developed nanomedicine comprising of Mn3O4 nanoparticles duly functionalized by biocompatible ligand citrate (C-Mn3O4 NPs) can maintain cellular redox balance in an animal model. We developed a cisplatin-induced CKD model in C57BL/6j mice where severe mitochondrial dysfunction resulting in oxidative distress lead to the pathogenesis. Four weeks of treatment with C-Mn3O4 NPs restored renal function, preserved normal kidney architecture, ameliorated overexpression of pro-inflammatory cytokines, and arrested glomerulosclerosis and interstitial fibrosis in CKD mice. A detailed study involving human embryonic kidney (HEK 293) cells and isolated mitochondria from experimental animals revealed that the molecular mechanism behind the pharmacological action of the nanomedicine involves protection of structural and functional integrity of mitochondria from oxidative damage, the subsequent reduction in intracellular ROS, and maintenance of cellular redox homeostasis. To the best of our knowledge, such studies that efficiently treated a multifaceted disease like CKD using a biocompatible redox nanomedicine are sparse in the literature. Successful clinical translation of this nanomedicine may open a new avenue in redox-mediated therapeutics of several other diseases (e.g., diabetic nephropathy, neurodegeneration, and cardiovascular disease) where oxidative distress plays a central role in pathogenesis.

pharmacology and toxicology↗

bioRxiv2020

Anti-GPR56 monoclonal antibody potentiates GPR56-mediated Src-Fak signaling to modulate cell adhesion

GPR56, also known as ADGRG1, is a member of the adhesion G protein-coupled receptor (aGPCR) family shown to play important roles in cell adhesion, brain development, immune system function, and tumorigenesis. GPR56 is upregulated in colorectal cancer and high expression correlates with poor prognosis. Several studies have shown that GPR56 couples to the G12/13 class of heterotrimeric G-proteins to promote RhoA activation. However, due to its structural complexity and lack of a high affinity receptor-specific ligand, the complete GPR56 signaling mechanism still remains largely unknown. To delineate the activation mechanism and intracellular signaling functions of GPR56, we generated a monoclonal antibody (mAb) which binds GPR56 with high affinity and specificity to the extracellular domain (ECD). We show that overexpression of GPR56 in 293T cells lead to increased phosphorylation of Src, Fak, and paxillin adhesion proteins and activation of the G12/13-RhoA-mediated serum response factor (SRF) pathway. Treatment of cells with anti-GPR56 mAb potentiated Src-Fak phosphorylation, RhoA-SRF signaling, and cell adhesion. Consistently, knockdown of GPR56 in colorectal cancer cells decreased Src-Fak pathway phosphorylation and cell adhesion. Interestingly, GPR56-mediated activation of Src-Fak phosphorylation occurred independent of RhoA, yet mAb-induced potentiation of RhoA-SRF signaling was Src-dependent. Furthermore, we show that the Serine-Threonine-Proline-rich (STP) region of the ECD of GPR56 was not essential for mAb binding, yet was required for activation of Src-Fak signaling. These data support a new ECD-dependent mechanism by which GPR56 functions to regulate cell adhesion through activation of Src-Fak signaling.

molecular biology↗