Biology subjects

Krishnan, N.

Publications and source records attributed to Krishnan, N..

At least 19 recordsLinked to original sources

bioRxiv2026

AutoWrinkleID: a machine learning pipeline for biofilm wrinkle identification and quantitative analysis

Biofilms are widely distributed in both natural and engineered systems and play a fundamental role in microbial ecology and biotechnological applications. When grown on agar substrates, biofilms often exhibit macroscopic structural features due to mechanical instabilities driven by matrix production. These wrinkles encode relevant information about biofilm growth and structural development and have even been shown to possess some functional roles. Despite their relevance, currently available approaches for wrinkle detection from images rely on manual annotation, which is time-consuming, not scalable, and strongly dependent on the annotator. In the present study, we developed an end-to-end machine learning pipeline, named AutoWrinkleID, that starts from bright field images of biofilms and performs wrinkle identification, characterisation, and quantification across multiple bacterial species and strains. The name reflects the automated identification and subsequent characterisation and quantification of biofilm wrinkles. The annotations used to generate the masks, namely images containing only the wrinkle structures, were obtained both through manual labelling and using constitutive fluorescence and motility fluorescence. Interestingly, we found that models trained using only manual annotations perform worse than those trained using motility fluorescence markers. A comparison between motility and constitutive fluorescence masks further indicates that motility based annotations consistently outperform constitutive fluorescence across all strains, strongly suggesting that motile phenotypes are tightly associated with wrinkle structures. Additional computational analysis is conducted on the same dataset to assess the robustness and limitations of the results as a function of training dataset. We also observed that Sholl analysis, originally developed for the study of neuronal dendrites and later applied to wrinkle analysis, can effectively characterize wrinkle patterns, although its applicability is strongly limited by wrinkle shape and by the quality of the masks.

biophysics↗

bioRxiv2026

Metabolic inhibition can enable compact physical integration of microbial partners

Microbes often generate by-products that inhibit own or consortial growth. Such imposing constraints can be alleviated by symbiotic partnerships where the partner consumes the limiting factor resulting in mutually beneficial cooperation. Theories of mitochondrial origin envisage such metabolic syntrophy of partners as the initial interaction, often coupled with mechanistic membrane gymnastics to trap the alphaproteobacterial symbiont to ensure vertical inheritance and as a prerequisite or vestibule of endosymbiosis. Yet we do not know how this happened. Here, using a mathematical model, we investigate how such metabolic self-inhibition enables and facilitates the evolution of compact physical integration between syntrophic partners. We show that when one species produces a metabolite that is self-inhibitory, selection favors increasingly tight spatial association of a detoxifying partner to mitigate local accumulation of the self-limiting product. Under a broad parameter range, this process drives the emergence of surface-associated configurations promoting morphological adaptations such as membrane protrusions or invaginations that increase inter-partner contact area. Our results prove that such costly host membrane contortions can evolve as a means to improve benefits of inhibition reduction by protective syntrophic ectosymbionts. Additionally, a unilateral syntrophic interaction between parties is sufficient for the transition; a mutualistic (or bilateral) one is not necessary. Our model establishes a direct evolutionary link between metabolic coupling and physical integration, suggesting that the need to alleviate (self-generated) inhibition can be a primary driver of ectosymbiotic attachment and its transition toward more intimate associations. Our findings provide a general theoretical framework for understanding how microbial consortia evolve structural complexity from initially loose metabolic interactions, with implications for the origins of stable symbioses and the early steps toward cellular integration.

evolutionary biology↗

bioRxiv2026

Stereotypical interciliary contacts in a C. elegans sense organ

Physical interactions among cells and their processes are critical for intercellular communication and the generation of ordered tissue patterns. Primary cilia projecting from the cell surface have recently been shown to form contacts with the processes of diverse cell types, as well as with other cilia, in the brain and other organs. Whether these ciliary contacts are established in an instructive manner or are formed passively due to physical proximity is unclear. Ultrastructural analyses previously showed that the cilia of a subset of sensory neurons in the head amphid organs of C. elegans exhibit interciliary contacts within a glia-defined channel. Here we show that these ciliary contact patterns are stereotyped and can be established in the absence of neighboring cilia, indicating that these associations may not simply reflect relative positioning within the amphid channel. We show that mutations in genes implicated in ciliary protein trafficking, ciliary membrane phospholipid composition, and cilia-cell interactions disrupt cilia structure and/or interciliary contacts, and that in a subset of mutants, cilia with altered morphologies can nevertheless establish correct contacts. Together, our findings suggest that cilia-cilia interactions within a sense organ are established via instructive mechanisms, and raise the possibility that cellular functions may be modulated by cilia-mediated intercellular communication. SummaryThis work investigates how primary cilia, structures that detect and transmit signals, form contacts with one another in a head sensory organ of the nematode Caenorhabditis elegans. The authors found that these contacts follow consistent patterns and can form even when neighboring cilia are absent, suggesting they are actively established rather than occurring due to physical proximity. The authors identified mutations in genes that regulate cilia protein content, membrane composition, and cellular adhesion that disrupt cilia structure or contacts. These findings suggest that cilia-cilia interactions are regulated, raising the possibility that they play important roles in cell communication.

cell biology↗

bioRxiv2026

BCLAF1 links RNA splicing to ATF4-dependent metabolic adaptation in acute myeloid leukemia

Acute myeloid leukemia (AML) is driven by a combination of genetic alterations and non-mutational mechanisms that disrupt normal hematopoiesis and support leukemic cell survival. While the mutational landscape of AML is well characterized, the non-genetic processes that sustain leukemic maintenance remain comparatively less understood. Using human AML cell lines and murine models of AML, we identify BCL2-associated transcription factor 1 (BCLAF1) as a key regulator of leukemic progression through control of mRNA processing. BCLAF1 physically associates with core spliceosome components and regulates alternative splicing, with a predominant effect on intron retention. We demonstrate that BCLAF1 is required for the productive splicing of activating transcription factor 4 (ATF4) mRNA, thereby sustaining ATF4 protein expression. Loss of BCLAF1 reduces ATF4 protein levels, leading to downregulation of metabolic target genes and disruption of de novo amino acid biosynthesis. Furthermore, depletion of BCLAF1 sensitizes AML cells to venetoclax, a clinically relevant BCL-2 inhibitor. Together, these findings uncover a previously unrecognized role for BCLAF1 in coordinating mRNA splicing and metabolic adaptation in AML, highlighting its potential as a therapeutic target. Statement of significanceAberrant RNA splicing and metabolic reprogramming are hallmarks of cancer, yet how these processes are mechanistically linked remains unclear. This study identifies BCLAF1 as a key regulator connecting splicing control to amino acid metabolism in acute myeloid leukemia, revealing a previously unrecognized functional vulnerability at the intersection of these pathways.

cancer biology↗

bioRxiv2025

Experience-dependent reconfiguration of receptors at a sensory compartment regulates neuronal plasticity

Neurons continuously adjust their properties as a function of experience. Precise modulation of neuronal responses is achieved by multiple cellular mechanisms that operate over a range of timescales. Primary sensory neurons rapidly adapt their sensitivities via posttranslational mechanisms including regulated trafficking of sensory molecules1-4 but also alter their transcriptional profiles on longer timescales to adapt to persistent sensory stimuli5-8. How diverse transcriptional and posttranscriptional pathways are coordinated in individual sensory neurons to accurately adjust their functions and drive behavioral plasticity is unclear. Here we show that temperature experience modulates both transcription and trafficking of thermoreceptors on different timescales in the C. elegans AFD thermosensory neurons to regulate response plasticity. Expression of the PY motif-containing adaptor protein (PYT-1) as well as the GCY-18 warm temperature-responsive guanylyl cyclase thermoreceptor9 is transcriptionally upregulated in AFD upon a temperature upshift5,10. We find that as GCY-18 begins to accumulate at the AFD sensory endings, the GCY-23 cooler temperature-responsive thermoreceptor9 exhibits altered subcellular localization and increased retrograde trafficking, thereby increasing the functional GCY-18 to GCY-23 ratio in the AFD sensory compartment. Altered GCY-23 localization and trafficking requires PYT-1-dependent endocytosis, and we show that PYT-1-mediated modulation of the GCY-18 to GCY-23 protein ratio at the AFD sensory endings is necessary to shift the AFD response threshold towards warmer values following the temperature upshift. Our results describe a mechanism by which transcriptional and posttranscriptional mechanisms are temporally coordinated across sensory receptors to fine tune experience-dependent plasticity in the response of a single sensory neuron type.

neuroscience↗

bioRxiv2025

An enteric neuron-expressed variant ionotropic receptor detects ingested salts to regulate salt stress resistance

The detection of internal chemicals by interoceptive chemosensory pathways is critical for regulating metabolism and physiology. The molecular identities of interoceptors, and the functional consequences of chemosensation by specific interoceptive neurons remain to be fully described. The C. elegans pharyngeal neuronal network is anatomically and functionally homologous to the mammalian enteric nervous system. Here, we show that the I3 pharyngeal enteric neuron responds to cations via an I3-specific variant ionotropic receptor (IR) to regulate salt stress tolerance. The GLR-9 IR, located at the gut lumen-exposed sensory end of I3, is necessary and sufficient for salt sensation, establishing a chemosensory function for IRs beyond insects. Salt detection by I3 protects specifically against high salt stress, as glr-9 mutants show reduced tolerance of hypertonic salt but not sugar solutions, with or without prior acclimation. While cholinergic signaling from I3 promotes tolerance to acute high salt stress, peptidergic signaling from I3 during acclimation is essential for resistance to a subsequent high salt challenge. Transcriptomic analyses show that I3 regulates salt tolerance in part via regulating the expression of osmotic stress response genes in distal tissues. Our results describe the mechanisms by which chemosensation mediated by a defined enteric neuron regulates physiological homeostasis in response to a specific abiotic stress.

neuroscience↗

bioRxiv2024

Inverted topologies in sequential fitness landscapes enable evolutionary control

Adaptive populations rarely evolve in a static environment. Therefore, understanding and ultimately controlling the evolution of a population requires consideration of fluctuating selective pressures. The fitness landscape metaphor has long been used as a tool for representing the selective pressures a given environment imposes on a population. Much work has already been done to understand the dynamics of evolution on a single fitness landscape. More recently, evolution on fluctuating or sequentially applied landscapes has come to the fore of evolutionary biology. As more empirical landscapes are described, metrics for describing salient features of paired landscapes will have uses for understanding likely evolutionary dynamics. Currently, Pearson correlation coefficient and collateral sensitivity likelihoods are used to quantify topographical relatedness or dissimilarity of a pair of landscapes. Here, we introduce the edge flip fraction, a new metric for comparing landscapes, which quantifies changes in the directionality of evolution between pairs of fitness landscapes. We demonstrate that the edge flip fraction captures topographical differences in landscapes that traditional metrics may overlook which have important consequences for the trajectories of populations evolving on them. By applying this metric to both empirical and synthetic fitness landscapes, we show that it partially predicts the collateral sensitivity likelihoods and can inform the optimality of drug sequences. We show that optimal drug sequences that keep populations within lower fitness regions require shifts in evolutionary directions, which are quantified by the edge flip fraction. Edge flip fraction complements existing measures and may help researchers understand how populations evolve under changing environmental conditions, and could yield clues in the pursuit of evolutionary control.

evolutionary biology↗

bioRxiv2024

Electrogenic Dynamics of Biofilm Formation: Correlation Between Genetic Expression and Electrochemical Activity in Bacillus subtilis

Bacterial biofilms are structured microbial communities that play a big role in diverse processes such as nutrient cycling and bacterial pathogenesis. Biofilms are known for their electron transfer properties which are essential for metabolic processes, microbial survival, and maintaining redox balance. In this study, we investigated the electrogenic properties of Bacillus subtilis, a bacterial producer of electron-donating biofilms. Interdigitated gold electrodes were utilized to continuously measure the electrochemical activity of biofilm-forming B. subtilis cells as well as genetic mutants unable to create them (biofilm-deficient), over three days of growth. The formation of extracellular polymeric substances (EPS) and filamentous appendages was monitored via scanning electron microscopy (SEM). Chronoamperometry was used to assess electrochemical activity, which showed fluctuations in electrical current at specific time points in biofilm-forming cells. In contrast, biofilm-deficient cells showed no corresponding changes in current. Cyclic voltammetry (CV) revealed significant differences between the voltammograms of biofilm-forming and biofilm-deficient cells that were hypothesized to be a result of the reduction of secreted flavodoxin only in biofilm-forming cells. Electrochemical impedance spectroscopy (EIS) was also performed at various intervals and analyzed using an equivalent circuit model. We identified the presence of a charge transfer resistance (Rct) exclusively in biofilm-forming cells which correlated to the time of increased electrochemical activity measured using choronoamperometry. Finally, through confocal microscopy, we found that the expression of a gene involved in biofilm matrix formation, tasA, was correlated with the time where electrochemical charge transfer was measured. Altogether, these results indicate that electrochemical activity is primarily present in biofilm-forming cells rather than in biofilm-deficient mutants. By combining electrochemical and microscopic methods, a methodology was developed to continuously monitor the stages of biofilm formation through measurement of electrochemical activity, substantiating a correlation between the expression of biofilm genes and their electrochemical or redox activities. These data show that electrochemical activities within biofilms vary over time and there is a temporal relationship between these processes and the expression of genes responsible for biofilm development.

bioengineering↗

bioRxiv2024

Early eukaryogenesis by host-initiated obligate ectosymbiosis and metabolic inhibition

Microbial symbiosis is extremely common among metabolically coupled cells, and, presumably, gave rise to mitochondria. How such symbioses emerge, evolve and stabilize are unknown, especially in the prokaryotic domain, where endosymbioses are virtually nonexistent. Yet there is growing evidence suggesting that the eukaryotic cell emerged from such a prokaryotic partnership, where integration was not the result of phagocytotic inclusion (as in case of plastids) but of metabolic cooperation. While prokaryotes almost ubiquitously engage in metabolic syntrophy, it is unknown if such cooperation alone can enable stable, dependent ectosymbioses that could pave the road toward physical integration of parties. Here, we tested the hypothesis that free-living syntrophy can lead to stable ectosymbiosis between microbial partners, using an ecological mathematical model. Assuming an already syntrophic and asymmetric partnership of free-living hosts and symbionts, we investigated under what conditions obligate ectosymbiosis evolve. Our results show that reduced inhibition (of self-inhibiting metabolic products) over the contact surface of partners can stabilize the ectosymbiotic consortia against free-living forms. Furthermore, strong metabolic activity between the host and their ectosymbionts could facilitate obligacy in their physical association. The model points to the significance of the contact surface in the evolution of crucial endosymbiotic features. Our results support the hypothesis that cooperative, syntrophic microbes (especially prokaryotes) are capable of coevolving to form species-specific ectosymbiosis by means of reducing the inhibition of accumulating products, a necessary first step towards endosymbiotic integration. The model provides a plausible explanation on how common metabolic syntrophy can lead to physical integration of parties through gradual ectosymbiosis. Moreover, our work fills a gap between microbial cooperation models (assuming free-living species) and those that are concerned only with already concluded physical integration under a multilevel selection paradigm.

evolutionary biology↗

bioRxiv2023

A BCG Skin Challenge Model for Assessing TB Vaccines

Controlled Human infection models (CHIM) are valuable tools for assessing relevant biological activity in vaccine candidates, with the potential to accelerate Tuberculosis vaccine development into the clinic. Tuberculosis infection poses significant constraints on the design of a CHIM using the causative agent Mycobacterium tuberculosis. As a safer alternative, we propose a challenge model using the attenuated vaccine agent Mycobacterium bovis BCG as a surrogate for Mycobacterium tuberculosis, and intradermal (skin) challenge as an alternative to pulmonary infection. We have developed a unique non-invasive imaging system based on fluorescent reporters to quantitatively measure bacterial load over time, thereby determining a relevant biological vaccine effect. We assessed the utility of this model to measure the effectiveness of two TB vaccines: the currently licenced BCG and a novel subunit vaccine candidate. To assess the efficacy of the skin challenge model a pharmacometric model was built describing the decline of fluorescence over time. The results show that vaccination is a statistically significant factor which reduced the fluorescence readout of both fluorophores. The higher decline in vaccinated mice correlated with bacterial burden in the lungs. This supports the fluorescence output from the skin as a reflection of vaccine induced functional pulmonary immune responses. This novel non-invasive approach allows for repeated measurements from the challenge site, providing a dynamic readout of vaccine induced responses over time. This BCG skin challenge model represents an important contribution to the ongoing development of controlled challenge models for Tuberculosis.

microbiology↗

bioRxiv2023

Liquid channels within B. subtilis biofilms allow the escape of trapped clones and population rescue

Phenotypic heterogeneity is one of the hallmarks of the biofilm lifestyle, where even isogenic populations give rise to spatially organized and phenotypically distinct subpopulations. One such pattern is generated by the ability of several biofilm-forming bacteria to switch between a flagellated and a matrix producing state. Here, using Bacillus subtilis as a model system, we investigate the role of this switch during biofilm development on a solid-air interface. By comparing the matrix-flagella spatio-temporal patterns in wild-type biofilms with mixtures of flagella- and matrix-null mutants biofilms, we find that pattern formation does not require a phenotypic switch that enables individual cells to respond to the local environment, but can be explained by a completely stochastic switch coupled to a phenotype-dependent fitness landscape that selects phenotypes at the population level. Integration of experiments and physical models shows that the coexistence between flagellated and matrix-producing cells provides the population with enhanced resilience to environmental changes, by enabling cells to manipulate and harness the local morphological and transport properties within the biofilm. Our results not only reveal a new evolutionary advantage of phenotypic plasticity in biofilms, but also illustrate how the biology and ecology of these populations are intrinsically tied to their physical properties.

evolutionary biology↗

bioRxiv2023

Vimentin impacts centrosome function and microtubule acetylation

Cell polarity is important for controlling cell shape, motility, and cell division processes. Vimentin intermediate filaments are necessary for proper polarization of migrating fibroblasts and assembly of vimentin and microtubule networks is dynamically coordinated, but the precise details of how vimentin mediates cell polarity remain unclear. Here, we characterize the effects of vimentin on the structure and function of the centrosome and the stability of microtubule filaments in wild-type and vimentin-null mouse embryonic fibroblasts (mEFs). We find that vimentin mediates the structure of the pericentrosomal material, promotes centrosome-mediated microtubule regrowth, and increases the level of stable acetylated microtubules in the cell. Loss of vimentin also impairs centrosome repositioning during cell polarization and migration processes that occur during wound closure. Our results suggest that vimentin modulates centrosome structure and function as well as microtubule network stability, which has important implications for how cells establish proper cell polarization and persistent migration.

cell biology↗

bioRxiv2023

Coevolutionary Stability of Host-Symbiont Systems with Mixed-mode Transmission

The coevolution of hosts and symbionts based on virulence and mode of transmission is a complex and diverse biological phenomenon. We introduce a conceptual model to study the stable coexistence of an obligate symbiont (mutualist or parasite) with mixed-mode transmission and its host. The existence of evolutionarily and ecologically stable coexistence is analyzed in the framework of coevolutionary dynamics. Using an age-structured Leslie model for the host, we demonstrate how the obligate symbiont can modify the hosts life history parameters (survival and fecundity) and the long-term growth rate of the infected lineage. The evolutionary success of the symbionts is given by the long-term growth rate of the infected population (multi-level selection). When the symbiont is vertically transmitted, we find that the host and its symbiont can maximize the long-term growth rate of the infected lineage. Moreover, we provide conditions for the ecological and evolutionary stability of the resident host-symbiont pair in the coevolutionary model, which does not allow invasion by any rare mutants (each mutant dies out by ecological selection). We observed that ecological competition, clearing of infection, and density-dependent interactions could play a role in determining the criteria for evolutionary stability.

evolutionary biology↗

bioRxiv2022

Rab8-, Rab11-, and Rab35-dependent mechanisms coordinating lumen and cilia formation during Left-Right Organizer development

An essential process during Danio rerios left-right organizer (Kupffers Vesicle, KV) development is for the majority of developing KV cells to form a motile cilium that extend into the KV lumen. Left-right beating of motile cilia within the KV lumen directs fluid flow to establishment the embryos left-right axis. However, when KV cells start to form cilia and how cilia formation is coordinated with KV lumen formation has not been examined. We identified that nascent KV cells form cilia at their centrosomes at random intracellular positions that then move towards a forming apical membrane containing cystic fibrosis transmembrane conductance regulator (CFTR). Using optogenetic clustering approaches, we found that Rab35 positive membranes recruit Rab11 to modulate CFTR delivery to the apical membrane, which is required for lumen opening, and subsequent cilia extension into the lumenal cavity. Once the intracellular cilia reach the CFTR positive apical membrane, Arl13b-positive cilia extend and elongate in a Rab8 dependent manner into the forming lumen once the lumen reaches an area of 300 m2. These studies demonstrate the need to acutely coordinate Rab8, Rab11, and Rab35-mediated membrane trafficking events to ensure appropriate timing in lumen and cilia formation during KV development.

cell biology↗

bioRxiv2022

Genesis of Ecto-symbiotic features based on Commensalistic Syntrophy

The origin of eukaryotes and organellogenesis have been recognized as a major evolutionary transition and subject to in-depth studies. Acknowledging the fact that the initial interactions and conditions of cooperative behaviour between free-living single-celled organisms are widely debated, we narrow our scope to a single mechanism that could possibly have set-off multi-species associations. We hypothesize that the very first step in the evolution of such cooperative behaviour could be a single mutation in an ancestral symbiont genome that results in the formation of an ecto-commensalism with its obligate ancestral host. We investigate the ecological and evolutionary stability of inter-species microbial interactions with vertical transmissions as an association based on syntrophy (cross-feeding). To the best of our knowledge, this is the first time that a commensalistic model based on the syntrophy hypothesis is considered in the framework of coevolutionary dynamics and invadability by mutant phenotype into a monomorphic resident system.

evolutionary biology↗

bioRxiv2022

sMAP: An interactive microarray data analysis tool for early-stage researchers

Microarray data enables biologists to extract differentially expressed genes (DEGs) across multiple phenotypes. While several pipelines and tools exist to perform microarray data analysis, they are targeted to users with moderate to advanced computational understanding and lack an easy-to-use, interactive and dynamic methodology to perform analysis assisted with comprehensive learning resources. In this study, we developed an interactive application "sMAP" (Standard Microarray Analysis Pipeline) to make transcriptome microarray data analysis more accessible in learning environments and to enable the identification of significant pathological biomarkers. In a case study of colorectal cancer, we showed that sMAP enabled us to reproduce previous findings and discover relevant pathways. sMAP provides a comprehensive set of tutorials and learning documentation to help early-stage researchers. The latest URLs of sMAPs hosting, tutorial, and frequently updated documentation can be found at https://github.com/BI-STEM-Away/sMAP.

bioinformatics↗

bioRxiv2022

BRCA1 Hypermethylation In Sporadic Breast Cancers: Discovering A Novel Pathway To Tumorigenesis Via Coordinate NBR2 Deregulation And TNBC Transformation

Women with a family history of mutations in the Breast cancer susceptibility gene, BRCA1 will have an increased risk of developing breast neoplasms. However, majority of the breast cancers are sporadic where BRCA1 mutations are very rare. Instead, 5-65% of sporadic cases manifest BRCA1 promoter hypermethylation and 30-40% of such cases develop into Triple Negative Breast Cancers. Even then, the molecular mechanism of BRCA1 hypermethylation mediated breast tumorigenesis has remained an enigma till date. Here, we present a novel tumorigenesis pathway for breast cancers that engenders from BRCA1 hypermethylation by generating site-specific methylations in the BRCA1 promoter using a modified version of CRISPR technology. We report that induction of site-specific methylation on BRCA1 promoter effectuates a downregulation in BRCA1 expression via alteration in the balance between its alternate transcripts {beta} and . Induced BRCA1 hypermethylation is also responsible for the attenuation of a long noncoding RNA, NBR2 (Neighbour of BRCA1 gene 2), which is transcribed through the bidirectional BRCA1 promoter in the reverse direction. Downregulation of NBR2 activates a feedback loop by leading to further downregulation of BRCA1 which is more evident under glucose starvation conditions and is associated with impaired DNA damage repair. BRCA1 hypermethylation also results in significant overexpression of {beta}-hCG (human chorionic gonadotrophin), which was found to be associated with highly aggressive and drug-resistant forms of BRCA1 mutated breast cancers invitro & in vivo in our previous study. Further, we report a change in the hormone receptor levels as the tumor progresses which demonstrates how BRCA1 deficient cells modulate their expression of ER- and ER-{beta} to promote their proliferation in early stages of tumor development and at later stages, transform to a basal tumor subtype by shedding down the expression of ER- & PR. Interestingly, we also discovered that modulation of ER- expression upon BRCA1 hypermethylation is responsible for the alteration in BRCA1 transcript ratio. Finally, in in vivo mouse studies, BRCA1 hypermethylated tumors were found to be much larger, aggressive and invasive as compared to wildtype, BRCA1 and NBR2 knockdown tumors with downregulation of ER- and PR; which explains the most probable reason behind high relapse rates in BRCA1 hypermethylated tumors. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/490082v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1c81155org.highwire.dtl.DTLVardef@1ea1fdcorg.highwire.dtl.DTLVardef@1d1b5e9org.highwire.dtl.DTLVardef@fddd22_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Lipid mediated inhibition of Niemann-Pick C1 protein is an evolutionary conserved feature of multiple Mycobacterium lineages and non-tubercular mycobacteria.

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB) and is a major cause of human morbidity and mortality. Crucially, Mtb can persist and replicate within host macrophages (M[FE]) and subvert multiple antimicrobial defense mechanisms. How this is achieved is incompletely understood. Previously, we reported that lipids shed by persistent mycobacteria inhibit NPC1, the lysosomal protein deficient in most cases of the rare, inherited lysosomal storage disorder Niemann-Pick disease type C (NPC). Inhibition of NPC1 leads to a drop in lysosomal calcium levels blocking phagosome-lysosome fusion and thereby leads to mycobacterial persistence. Studies of mycobacterial lineages have identified events during mycobacterial evolution that result in the acquisition of persistence. We speculated that the production of specific cell wall lipid(s) capable of inhibiting NPC1 activities could have been a critical step in the evolution of pathogenicity. In this study, we have therefore investigated whether lipid extracts from clinical Mtb strains representative of multiple Mtb lineages, members of the Mtb complex (MTBC) and selected non-tubercular mycobacteria (NTM) inhibit the NPC pathway. We have found that the ability to inhibit the NPC pathway was present in all clinical isolates studied from Mtb lineages 1, 2 and 4. We also found that lipids from MTBC member, Mycobacterium bovis and the NTM, Mycobacterium abscessus and Mycobacterium avium also inhibited the NPC pathway. However, when lipids were assayed from Mycobacterium canettii (M. canettii), a smooth tubercle mycobacterium, which is considered to resemble the common ancestor of the MTBC no inhibition of the NPC1 pathway was detected. We therefore conclude that the evolution of mycobacterial cell wall lipids that inhibit the NPC pathway evolved early and post divergence from M. canettii related mycobacteria and NPC1 inhibition significantly contributes to the ability of these pathogens to persist and cause disease. Authors summaryMycobacterium tuberculosis (Mtb) actively modifies the hostile intracellular environment of host cells to create a niche in which it can persist and replicate. How this is accomplished is incompletely understood. We previously reported an unexpected phenotypic similarity between cells infected with pathogenic mycobacteria and those of the rare, neurodegenerative lysosomal storage disorder, Niemann-Pick disease type C (NPC). Mechanistically, we showed that pathogenic mycobacteria shed lipids that inhibit NCP1, the lysosomal membrane protein that is dysfunctional in NPC and thereby establish conditions that favour their survival. In this study, we have investigated the phylogenetic distribution of lipids that inhibit NPC1. We have screened lipid extracts from multiple clinical mycobacterial isolates representing different Mtb lineages, other members of the Mtb complex and non-tuberculous mycobacteria for their ability to induce NPC phenotypes. We detected activity in all of the groups tested, but not from Mycobacterium canettii, which is believed to resemble the ancestral species. These data indicate that targeting of NPC1 to achieve intracellular persistence evolved early in the evolution of the Mtb complex, but after divergence from the presumed ancestral species.

microbiology↗