Biology subjects

Chidambaram, S. B.

Publications and source records attributed to Chidambaram, S. B..

10 recordsLinked to original sources

bioRxiv2026

Targeting AATF reprograms the tumor microenvironment and suppresses hepatocellular carcinoma via MIR100HG TGFβ signaling

Hepatocellular carcinoma (HCC), a leading cause of cancer death, has a dynamic and heterogeneous tumor microenvironment (TME) that drives progression and therapeutic resistance. We previously elucidated that apoptosis antagonizing transcription factor (AATF) drives angiogenesis in HCC. However, its role in TME remains unexplored. We employed an orthotopic xenograft mouse model, implanting human HCC cells into the liver, and achieved liver-specific silencing via tail vein injection of AAV8 carrying mouse-specific siAATF or siControl. Histological, biochemical, and molecular analyses, combined with whole-genome transcriptomics mapped to mouse and human genomes, were used to study TME and tumor compartments separately. Silencing of AATF in the TME significantly reduced tumor growth compared with controls. Furthermore, AATF loss disrupted key processes in TME, including inflammation, immune response, angiogenesis, and extracellular matrix remodeling. Mechanistically, TGF-{beta} signaling was significantly suppressed in the TME, thereby affecting tumor cell cycle and metabolic activity, ultimately leading to tumor regression. The long noncoding RNA (lncRNA) analysis identified MIR100HG as a key downstream regulator of AATF in the TGF-{beta} signaling pathway. These findings expand the oncogenic role of AATF to include regulation of the TME via the AATF-MIR100HG-TGF-{beta} axis, highlighting its potential as a therapeutic target in HCC.

cancer biology↗

bioRxiv2025

Examining Sleep Signals at the Cradle of Life: Can phylogenomic analysis of the Last Universal Common Ancestor (LUCA) reveal the fundamental role of sleep?

In common with most physiological activities, sleep is a highly evolutionarily conserved function. Nevertheless, the purpose of sleep remains inadequately investigated. One possible cause of this deficiency is the limitations of the traditional methods used for examining sleep. Up to this time, the mainstay tool used to look at the evolutionary basis of sleep has been phylogenetic analysis. This approach has provided many valuable insights into sleep, yet it has left many questions unanswered. The present study uses a relatively new hybrid technique at the interface of phylogenetics and genomics, known as phylogenomic analysis. This study is the first to use phylogenomic analysis to investigate the basis of sleep by evaluating the presence and conservation of sleep-related genes in the reconstructed genome of the Last Universal Common Ancestor (LUCA). Our gene set enrichment analysis of humans and LUCA indicates that the conserved sleep genes are linked to signaling, metabolism, and circadian rhythm pathways, suggesting that these genes possess primordial roles in essential physiological functions. These findings indicate that the component genes carry out essential physiological tasks that were subsequently repurposed to regulate sleep in more advanced organisms throughout evolution. This study lays the foundation for a systematic phylogenomic exploration of sleep-related genes, connecting molecular evolution with sleep science. By tracing the biological history of sleep to its deep evolutionary origins, our research presents novel insights into sleeps nature, origin, and evolutionary function, paving the way for further interdisciplinary exploration of the biology of sleep. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/644522v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@17adc89org.highwire.dtl.DTLVardef@124de86org.highwire.dtl.DTLVardef@18d3e5corg.highwire.dtl.DTLVardef@1f93b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Studying sleep orthologs in Epsilonproteobacteria through an evolutionary lens: Investigating sleep mysteries through phylogenomics

The current study employed phylogenomic methods to examine the evolutionary role and significance of sleep-related genes in Sulfurimonas paralvinellae of the Epsilonproteobacteria class. This has facilitated the identification of conserved sleep orthologs, including DnaK, serine hydroxymethyltransferase, and potassium channel family proteins, exhibiting sequence similarities ranging from 39.13% to 61.45%. These findings align with prior research indicating that chaperones and ion channels are conserved during sleep. This was demonstrated by the observation that proteins with fewer domains exhibited more significant conservation than others, such as adenylate kinase, which is substantial under selective pressure. Distinct adaptations in bifunctional protein - serine/threonine kinases and phosphatases were linked to S. paralvinellae, an extremophilic organism adapted to high-pressure and/or high-temperature conditions, indicating functional divergence influenced by the organisms environment. The Gene Ontology study results indicated catalytic activity, potassium channel function, and cellular processes, underscoring the significance of ion channels in regulating the sleep-wake cycle. Furthermore, the categories not recognized as particularly significant for the over-represented genes encompassed metabolic and signal transduction categories, suggesting enhanced functional flexibility within this protein subfamily. The findings emphasize that orthologous interactions are complex and influenced by subfunctionalization and neofunctionalization of ecology and evolution. These findings enhance the existing understanding of the evolution of sleep-related genes and their association with metabolic and environmental changes, providing a foundation for subsequent experimental investigations and cross-taxonomic comparisons.

genomics↗

bioRxiv2024

Unraveling the Mysteries of Sleep: Exploring Phylogenomic Sleep Signals in the Recently Characterized Archaeal Phylum Lokiarchaeota near Loki's Castle

Sleep is a universally conserved behavior with an elusive origin and an uncertain evolutionary purpose. Leveraging phylogenomics, we investigate the evolutionary foundations of sleep by identifying orthologs of Human sleep-related genes in the Lokiarchaeota of the Asgard superphylum. Our findings indicate a conserved suite of genes associated with energy metabolism and cellular repair, suggesting a primordial role of sleep in cellular maintenance. This data lends credence to the idea that sleep improves organismal fitness across evolutionary time by acting as a restorative process. Notably, our approach demonstrates that phylogenomics is more useful than standard phylogenetics for clarifying common evolutionary traits. By offering insight into the evolutionary history of sleep and putting forth a novel model framework for sleep research across taxa, these findings contribute to our growing understanding of the molecular foundation of sleep. This study lays the groundwork for further investigations into the importance of sleep in various organisms, which could have consequences for human health and a deeper comprehension related to the fundamental processes of life. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/621620v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@4dd502org.highwire.dtl.DTLVardef@1db82c5org.highwire.dtl.DTLVardef@6662d3org.highwire.dtl.DTLVardef@1e2268b_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Cross-Kingdom Genomic Conservation of Human Sleep-Related Gene Orthologs: Phylogenomic Evidence from Chlamydomonas reinhardtii

Sleep is a widespread and evolutionarily conserved process observed in diverse organisms, from jellyfish to mammals, hinting at its origin as a life-supporting mechanism over 500 million years ago. Although its fundamental purpose and mechanisms remain unclear, the evolution and adaptive significance of sleep continue to be debated. This study explores the evolutionary origins of sleep using Chlamydomonas reinhardtii as a model organism, identifying 145 orthologs analogous to known sleep-related genes across species, highlighting the evolutionary conservation of sleep-regulating pathways. Additionally, discovering uncharacterized proteins with high sequence similarity and significant e-values suggests unexplored roles in sleep regulation, underscoring the potential of C. reinhardtii to reveal new insights into the molecular basis of sleep. This work provides a foundation for identifying previously unknown sleep-associated proteins, particularly within single-celled organisms, which may offer novel perspectives on the biological role of sleep. The study demonstrates that phylogenomic analysis of diverse model organisms can expand our understanding of the evolutionary trajectory of sleep and its fundamental function, paving the way for further research in sleep biology and its health implications. Overall, the fundamental functions of sleep observed in higher animal phyla originated from its primordial activities, demonstrating an evolutionary continuum wherein more specialized tasks were integrated with sleeps essential restorative properties.

bioinformatics↗

bioRxiv2024

Green Jackfruit Flour Prevents Metabolic Dysfunction-Associated Steatohepatitis and Progression to Hepatocellular Carcinoma via the AMPK and MAPK Signaling Pathways

Metabolic dysfunction-associated steatotic liver disease (MASLD), encompassing metabolic-dysfunction associated steatotic liver (MAFL) and steatohepatitis (MASH), which further progresses to hepatocellular carcinoma (HCC), is a serious public health concern. Given the paucity of approved therapeutic strategies for this lifestyle disorder, dietary interventions may prove effective. We evaluated how green jackfruit flour (JF) prevents MASH and progression to HCC and its underlying mechanisms. The study utilized two murine models that mimicked human MASLD disease: (i) a diet-induced MASH model; (ii) a MASH-HCC model induced by diet and a very low dose of CCl4. C57Bl/6 mice were fed with chow (CD) or western diet (WD) with normal (NW) or sugar water (SW) for 12 weeks, then randomized to receive either 5 kcal% green jackfruit flour (JF) or an equal volume of placebo flour (PB). The biochemical, histological, and molecular analyses were assessed. JF significantly reduced body weight, liver injury, insulin resistance, and alleviated obesity, steatosis, inflammation, fibrosis, and tumor development in WDSW or WDSW/CCl4 mice compared to placebo groups. Furthermore, JF activated AMPK (AMP-activated protein kinase) and inhibited MAPK (mitogen-activated protein kinase) signaling pathways in MASH and MASH-HCC experimental models, respectively. This was supported by sodium propionate treatment, the primary short-chain fatty acid entering the liver from JFs soluble fiber microbial fermentation, which also regulated AMPK and MAPK signaling in cellular models of MASH and HCC, respectively. Hence, our findings present strong evidence of JFs therapeutic potential in the prevention of MASH and MASH-HCC, warranting further investigation of JFs efficacy as a dietary intervention in clinical trials.

cancer biology↗

bioRxiv2023

Curcumin Ameliorates AATF-mediated Liver Damage and Inflammation to Cancer in NASH-HCC

In tandem with the expanding obesity pandemic, the prevalence of metabolic dysfunction associated steatohepatitis (MASH, formerly known as NASH)-driven hepatocellular carcinoma (HCC) is predicted to rise globally, creating a significant need for therapeutic interventions. We previously identified the upregulation of apoptosis antagonizing transcription factor (AATF), which is implicated in facilitating the progression from MASH to HCC. The objective of this study was to examine whether the intervention of curcumin could alleviate AATF-mediated MASH, inhibit tumor growth, and elucidate the underlying mechanism. A preclinical murine model mimicking human MASH-HCC was employed, subjecting mice to either a chow diet normal water (CDNW) or western diet sugar water (WDSW) along with very low dose of carbon tetrachloride (CCl4-0.2 l/g, weekly). Mice receiving curcumin (CUR) alongside WDSW/CCl4 exhibited significant improvements, including reduced liver enzymes, dyslipidemia, steatosis, inflammation, and hepatocellular ballooning. Curcumin treatment also suppressed hepatic expression of inflammatory, fibrogenic, and oncogenic markers. Of note, there was a significant reduction in the expression of AATF upon curcumin treatment in WDSW/CCl4 mice and human HCC cells. In contrast, curcumin upregulated Kruppel-like factor 4 (KLF4) in MASH liver and HCC cells, which is known to downregulate sp1 (specificity protein-1) expression. Thus, curcumin treatment effectively inhibited the progression of MASH to HCC by downregulating the expression of AATF via the KLF4-Sp1 signaling pathway. These preclinical findings establish a novel molecular connection between curcumin and AATF in reducing hepatocarcinogenesis, and provide a strong rationale for the development of curcumin as a viable treatment for MASH-HCC in humans.

cancer biology↗

bioRxiv2022

Tecomella undulata Improves Insulin Sensitivity by Attenuating Inflammation and Oxidative Stress in Experimental NASH

Background and AimThe pathophysiology of NASH is complex owing to its diverse pathological drivers, and until recently, there were no approved drugs for this disease. Tecomella undulata is a popular herbal medicine used to treat hepatosplenomegaly, hepatitis, and obesity. However, the potential role of Tecomella undulata in NASH has not yet been scientifically investigated. Experimental ProcedureMice fed with chow diet and normal water (CDNW) or western diet and sugar water (WDSW) for 12 weeks were randomized to receive vehicle control, Saroglitazar, or Tecomella undulata for an additional 12 weeks. Insulin resistance, lipid profiles, histological analysis, and liver enzymes were assessed. The oxidative stress, ER and inflammatory markers were determined by quantitative RT-PCR (qRT-PCR) and western blot analysis. Results and ConclusionThe administration of Tecomella undulata via oral gavage lowered body weight, insulin resistance, alanine transaminase (ALT), aspartate transaminase (AST), triglycerides, and total cholesterol in WDSW mice but had no effect on CDNW mice. Tecomella undulata improved steatosis, lobular inflammation, and hepatocyte ballooning and resolved NASH in WDSW mice. Furthermore, Tecomella undulata also alleviated the WDSW-induced ER stress and oxidative stress, enhanced antioxidant status, and thus reduced inflammation in the treated mice. Of note, these effects were on par with Saroglitazar, the approved drug used to treat human NASH and positive control used in the study. Thus, our findings indicate the potential of Tecomella undulata to ameliorate WDSW-induced steatohepatitis, and these preclinical data provide a strong rationale for assessing Tecomella undulata for the treatment of NASH in humans.

physiology↗

bioRxiv2022

ALDH2 DEFICIENCY INCREASES SUSCEPTIBILITY TO BINGE ALCOHOL-INDUCED GUT LEAKINESS, ENDOTOXEMIA, AND ACUTE LIVER INJURY IN MICE THROUGH THE GUT-LIVER AXIS

Mitochondrial aldehyde dehydrogenase 2 (ALDH2) is the major enzyme responsible for metabolizing toxic acetaldehyde to acetate and acts as a protective or defensive protein against various disease states associated with alcohol used disorder (AUD), including alcoholic liver disease (ALD), and elevated oxidative stress. We hypothesized that Aldh2-knockout (KO) mice are susceptible to binge alcohol-mediated liver injury than wild-type (WT) mice through increased gut leakiness and endotoxemia. Therefore, this study aimed to investigate the protective role of ALDH2 in binge alcohol-induced gut permeability, endotoxemia, and acute inflammatory liver injury by exposing Aldh2-KO or WT mice to a single oral dose of binge alcohol 3.5, 4.0, or 5.0 g/kg. Our findings showed for the first time that ALDH2 deficiency in Aldh2-KO mice increases their sensitivity to alcohol-induced oxidative and nitrative stress, enterocyte apoptosis, and nitration of gut tight junction (TJ) and adherent junction (AJ) proteins, leading to their degradation. These resulted in gut leakiness and endotoxemia in Aldh2-KO mice after exposure to a single dose of ethanol even at 3.5 g/kg, while no changes were observed in the corresponding WT mice. The elevated serum endotoxin (lipopolysaccharide, LPS) and/or bacterial translocation contributed to systemic inflammation, hepatocyte apoptosis, and subsequently acute liver injury, indicating the disruption in the gut-liver axis. Furthermore, treatment with Daidzin, an ALDH2 inhibitor, exacerbated ethanol-induced cell permeability and reduced TJ/AJ proteins in T84 human colonic cells. These changes were reversed by Alda-1, an ALDH2 activator, indicating a crucial role of ALDH2 in protecting against alcohol-induced epithelial barrier dysfunction. All these findings suggest that ALDH2 deficiency or gene mutation in humans is a risk factor to alcohol-mediated gut and liver injury, and ALDH2 could be an important therapeutic target against alcohol-associated tissue/organ damage. HighlightsO_LIBinge alcohol increases oxidative and nitrative stress in the intestine and liver. C_LIO_LIBinge alcohol causes gut leakiness, endotoxemia, and acute liver injury. C_LIO_LILeaky gut is caused by elevated degradation of nitrated intestinal TJ/AJ proteins. C_LIO_LIAldh2-KO mice are susceptible to binge-alcohol-induced leaky gut and liver injury. C_LIO_LIALDH2 inhibition increases alcohol-induced T84 colonic epithelial cell permeability. C_LI

pharmacology and toxicology↗

bioRxiv2021

Inhibition of PDE4 by Roflumilast ameliorates sleep deprivation-induced cognitive dysfunction in C57BL/6J mice

Sleep deprivation (SD) interferes with long-term memory and cognitive functions by over-activation of phosphodiesterase (PDEs) enzymes. PDE4, a non-redundant regulator of the cyclic nucleotides (cAMP), is densely expressed in the hippocampus and is involved in learning and memory processes. In the present study, we investigated the effects of Roflumilast (ROF), a PDE4B inhibitor, on sleep deprivation induced cognitive dysfunction in a mouse model. Memory assessment was performed using a novel object recognition task and the hippocampal cAMP level was estimated by the ELISA method. The alterations in the expressions of PDE4B, amyloid-beta (A{beta}), CREB, BDNF, and synaptic proteins (Synapsin I, SAP 97, PSD 95) were assessed to gain insights into the possible mechanisms of action of ROF using the Western blot technique. Results show that ROF reversed SD induced cognitive decline in mice. ROF down-regulated PDE4B and A{beta} expressions in the brain. Additionally, ROF improved the cAMP level and the protein expressions of synapsin I, SAP 97, and PSD 95 in the hippocampal region of SD mice. Taken together, these results suggest that ROF can suppress the deleterious effects of SD-induced cognitive dysfunction via the PDE4B-mediated cAMP/CREB/BDNF signaling cascade.

pharmacology and toxicology↗