Biology subjects

Ramachandra, R.

Publications and source records attributed to Ramachandra, R..

7 recordsLinked to original sources

bioRxiv2026

NAMPT activation uncovers a senescence-specific vulnerability and promotes healthy aging in combination with NAM

Aging is driven by multiple interacting processes, suggesting that effective strategies to promote healthy aging may require simultaneous targeting of more than one underlying mechanism. Here we identify a strategy that couples restoration of nicotinamide adenine dinucleotide (NAD+) homeostasis with selective targeting of senescent cells, two mechanistically linked features of aging. Senescent cells express elevated intracellular levels of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the nicotinamide (NAM) salvage pathway for NAD+ biosynthesis. Despite increased NAMPT abundance, isotope-tracing studies revealed decreased NAD+ biosynthesis and consumption, indicating that elevated NAMPT abundance was not accompanied by a corresponding increase in NAD+ metabolic flux. Treatment with the NAMPT activator SBI-0802162 engaged the spare enzymatic capacity of NAMPT in senescent cells and produced a marked rise in intracellular NAD+ that, when sustained, disrupted their transcriptional program and selectively reduced the viability of senescent cells but not proliferating cells. In mice, SBI-0802162 reduced circulating NAM levels, suggesting that sustained NAMPT activation may be limited by substrate availability. This observation prompted the development of a combination approach using SBI-0802162 together with dietary NAM supplementation. Co-administration of SBI-0802162 and NAM robustly increased tissue NAD+, suppressed select age-associated inflammatory signatures and markers of cellular senescence in a tissue-specific manner. These molecular effects occurred alongside preserved physical performance in aged mice and reductions in food intake and body weight, which were observed whether SBI-0802162 was present in the chow or administered by oral gavage. Together, these findings establish a mechanistically integrated approach to target two convergent features of aging, NAD+ dysregulation and senescent cell accumulation, and support combined NAMPT activation and NAM supplementation as a strategy to promote healthy aging.

molecular biology↗

bioRxiv2025

ColorSTEM: An easy and convenient approach to Multicolor Electron Microscopy of Labeled Biological Specimens

A new method for Multicolor Electron Microscopy (EM) using scanning transmission EM, ColorSTEM has been developed to increase the sensitivity, instrument availability and ease of use compared to that previously developed using electron energy loss spectroscopy and energy filtered transmission EM. Both methods paint multiple subcellular complexes with different colors, enabled by the localized and targeted deposition of diaminobenzidine (DAB) conjugated to different metals, which provides the differentiating signal from each other. With ColorSTEM, elastic scattering that is dependent upon atomic weight (Z-contrast) has far greater signals. Using deposited DAB with copper or gold to label subcellular components, Z-contrast imaging generates a pseudo-elemental map, resulting from differences in the grayscale of the conventional STEM images.

cell biology↗

bioRxiv2025

A Phenotype-Driven Multi-Omic Atlas of Glioblastoma Invasion

BackgroundGlioblastoma (GBM) invasion is clinically decisive but difficult to model systematically. Existing patient-derived xenograft (PDX) resources rarely couple reproducible in vivo invasion phenotypes with matched multi-omic profiles at scale, limiting mechanistic insight and phenotype-informed therapeutic hypotheses. MethodsWe established the HGCC Phenobank, comprising 65 patient-derived GBM stem-like cultures with matched multi-omic profiling and orthotopic engraftment in 449 mice. Blinded histopathology quantified ten invasion traits per case. These phenotypes were integrated with RNA sequencing, DNA methylation, and mass-spectrometry-based proteomics. Multi-Omic Factor Analysis (MOFA) identified latent molecular programs. Phenotype-specific RNA signatures were matched to LINCS drug-perturbation profiles and validated in 3D gliomasphere and ex vivo brain-slice assays. ResultsTwo dominant, reproducible invasion modes emerged across models: diffuse parenchymal infiltration and perivascular/condensed growth. Proneural cultures formed more aggressive tumors in immunodeficient mice, and mouse survival showed a modest correlation with patient survival in matched cases (Pearson r = 0.1832, p = 0.045). MOFA identified 15 latent factors; Factor 1, enriched for ASCL1/OLIG1/OLIG2 programs and associated with TP53/DCHS2/WNK2 alterations, was linked to increased tumor formation, diffuse invasion, and shorter mouse survival, and stratified GBM patients in TCGA and in our matched patient cohort. Drug-signature matching separated mechanisms targeting diffuse versus perivascular invasion. Experimental validation confirmed phenotype-selective sensitivities, and inhibitors PIK-75 and buparlisib suppressed invasion dynamics across representative models in 3D and brain-slice assays. ConclusionsThe HGCC Phenobank provides the first openly available PDX resource that systematically links GBM invasion phenotypes to multi-omic programs and therapeutic predictions. This framework enables reproducible model selection, mechanistic dissection of invasion modes, and phenotype-guided therapeutic discovery. Key PointsO_LIDiffuse and perivascular invasion define orthogonal GBM axes C_LIO_LIASCL1/OLIG factor links initiation, diffuse growth, and survival C_LIO_LIPhenotype-matched drugs validated; PIK-75 and buparlisib curb invasion dynamics C_LI Importance of the StudyGlioblastoma invasion varies substantially between patients, yet existing patient-derived xeno-graft resources rarely combine reproducible in vivo phenotyping with matched multi-omic profiling at scale. The HGCC Phenobank addresses this gap with standardized, blinded scoring of ten invasion traits across 449 orthotopic xenografts from 65 molecularly characterized GBM stem-like cultures, integrated with transcriptomic, methylomic, and proteomic data. We identify two dominant, reproducible invasion modes and a cross-modal neurodevelopmental program, the ASCL1/OLIG1/2-associated Factor 1, that links tumor initiation, diffuse growth, and survival in mice, and stratifies GBM patients in TCGA and in our matched patient cohort. In a spatially resolved xenograft section, Factor 1 signal localizes to the invasive tumor periphery. By matching phenotype-specific RNA signatures to drug-induced transcriptional responses, we show that invasion phenotypes nominate selective vulnerabilities, exemplified by PIK-75. This openly shared resource enables reproducible model selection, mechanistic dissection of invasion programs, and phenotype-guided therapeutic discovery.

cancer biology↗

bioRxiv2023

Fe-TAMLs as a new class of small molecule peroxidase probes for correlated light and electron microscopy

We introduce Fe-TAML, a small molecule-based peroxidase as a versatile new member of the correlated fluorescence and electron microscopy toolkit. The utility of the probe is demonstrated by high resolution imaging of newly synthesized DNA (through biorthogonal labeling), genetically tagged proteins (using HaloTag), and untagged endogenous proteins (via immunostaining). EM visualization in these applications is facilitated by exploiting Fe-TAMLs catalytic activity for the deposition of localized osmiophilic precipitates based on polymerized 3,3-diaminobenzidine. Optimized conditions for synthesizing and implementing Fe-TAML based probes are also described. Overall, Fe-TAML is a new chemical biology tool that can be used to visualize diverse biomolecular species along nanometer and micron scales within cells.

cell biology↗

bioRxiv2020

Elemental Mapping of Labeled Biological Specimens at Intermediate Energy Loss in an Energy-Filtered TEM acquired using a Direct Detection Device

The multi-color or single-color EM that was developed previously, by the pseudo-colored overlay of the core-loss or high-loss EFTEM elemental map/s of the lanthanide onto the conventional image, the lanthanide chelates conjugated to diaminobenzidine being sequentially deposited as a result of selective oxidization by orthogonal photosensitizers / peroxidases. The synthesis of the new second generation lanthanide DABs, which contains 4 times more lanthanide per DAB, gives significant signal amplification and enabling collection of elemental maps at much lower energy-loss regions more favorable. Under the same experimental conditions, acquiring EFTEM elemental maps for the lanthanides at the lower energy-loss of N4,5 edge instead of the core-loss M4,5 edge, provides ~4x increase in signal-to-noise and ~2x increase in resolution. The higher signal at the N4,5 edge, also allows for more sophisticated technique of EFTEM spectrum Image for the acquisition of elemental maps with very high signal fidelity.

systems biology↗

bioRxiv2020

A genetic probe for visualizing glutamatergic synapses and vesicles by 3D electron microscopy

Communication between neurons relies on the release of diverse neurotransmitters, which represent a key-defining feature of a neurons chemical and functional identity. Neurotransmitters are packaged into vesicles by specific vesicular transporters. However, tools for labeling and imaging synapses and synaptic vesicles based on their neurochemical identity remain limited. We developed a genetically encoded probe to identify glutamatergic synaptic vesicles at the levels of both light and electron microscopy (EM) by fusing the mini singlet oxygen generator (miniSOG) probe to an intra-lumenal loop of the vesicular glutamate transporter-2. We then used a 3D imaging method, serial block face scanning EM, combined with a deep learning approach for automatic segmentation of labeled synaptic vesicles to assess the subcellular distribution of transporter-defined vesicles at nanometer scale. These tools represent a new resource for accessing the subcellular structure and molecular machinery of neurotransmission and for transmitter-defined tracing of neuronal connectivity.

neuroscience↗

bioRxiv2018

Split-miniSOG for detecting and localizing intracellular protein-protein interactions: application to correlated light and electron microscopy

A protein complementation assay (PCA) for detecting and localizing intracellular protein-protein interactions (PPIs) was built by bisection of miniSOG, a fluorescent flavoprotein derived from the light, oxygen, voltage (LOV)-2 domain of Arabidopsis phototropin. When brought together by interacting proteins, the fragments reconstitute a functional reporter that permits tagged protein complexes to be visualized by fluorescence light microscopy (LM), and then by standard as well as \"multicolor\" electron microscopy (EM) imaging methods via the photooxidation of 3-3-diaminobenzidine (DAB) and its lanthanide-conjugated derivatives.

cell biology↗