Biology subjects

Malla, S.

Publications and source records attributed to Malla, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatial Metabolic Modeling Reveals Zinc–Citrate Rewiring and Therapeutic Vulnerabilities in Prostate Cancer

Prostate cancer exhibits a metabolic phenotype distinct from the Warburg paradigm, characterized by reprogramming of the zinc-citrate secretory axis that normally drives citrate accumulation and secretion in prostatic epithelium. How this metabolic rewiring is organized across the spatial architecture of tumors and linked to androgen receptor (AR) signaling remains poorly understood. We integrated spatial transcriptomics data from twelve regions spanning normal, inflamed, and Gleason-graded prostate tissues with genome-scale metabolic modeling to quantify metabolic activity across tissue states. The analysis identified the zinc-citrate-aconitase axis as a central feature of prostate cancer metabolic reprogramming, linking increased aconitase activity to enhanced citrate export, acetyl-CoA generation, and de novo lipogenesis. Metabolic similarity was more strongly associated with spatial proximity than with histological classification, suggesting field-level metabolic reprogramming beyond visible pathological boundaries. AR activity displayed grade-dependent associations with lipid metabolic pathways, indicating heterogeneous coupling between androgen signaling and metabolism across tumor regions. Consistent with the established biology of prostate cancer, predicted flux distributions did not support a classical Warburg phenotype. A flux-based target prioritization framework identified HMGCR, FASN, and SLC25A1 as candidate therapeutic targets, with independent support from TCGA-PRAD expression profiles and DepMap CRISPR essentiality data. Together, these findings provide a spatially resolved view of prostate cancer metabolism, establish the zinc-citrate axis as a dominant feature of metabolic organization, and identify candidate metabolic vulnerabilities for therapeutic intervention.

Cancer Biology↗

bioRxiv2026

Solute Carrier Transporter Family Modulates Neutrophil Metabolism During Health and Disease

Neutrophils are the most abundant leukocytes in humans and play a central role in immune regulation. Although traditionally viewed as terminally differentiated cells with limited plasticity, growing evidence indicates that neutrophils exhibit substantial functional heterogeneity in response to stress. To date, however, most studies have focused on transcriptional and signaling changes, while metabolic heterogeneity, especially beyond central carbon metabolism, remains poorly characterized. Here, we systematically investigate metabolic reprogramming in neutrophils under three stress conditions: granulocyte colony-stimulating factor (G-CSF) treatment, hematopoietic stem cell transplantation (HSCT), and pancreatic ductal adenocarcinoma (PDAC). Using condition-specific genome-scale metabolic (GSM) models, we identify distinct metabolic vulnerabilities across neutrophil states. Vitamin metabolism emerged as a key differentiating feature between G-CSF- and HSCT-treated neutrophils, whereas PDAC-associated neutrophils displayed globally enhanced metabolic activity coupled with restricted metabolite exchange fluxes. Furthermore, solute carrier (SLC) family transporters were identified as major metabolic regulators underlying stress-induced neutrophil reprogramming. Together, our findings demonstrate that neutrophil heterogeneity extends beyond transcriptional programs to encompass profound metabolic specialization, highlighting metabolism as a critical dimension of neutrophil plasticity in health and disease.

immunology↗

bioRxiv2026

Phenotype-dependent subtyping exposes high MYC activity as a targetable dependency in LuAd

C-MYC (MYC) occupies a critical nexus of oncogenic signalling and deregulated expression of MYC is widespread across most human cancer types, suggesting that MYC should be an attractive target for therapeutic intervention. Although 30-40% of human Non-Small Cell lung cancers show low level amplification of c-MYC and genetic evidence has shown that c-Myc is a key downstream effector of KRas-driven lung tumourigenesis in mouse models, the functional contribution of MYC to human lung cancer remains unclear. We applied a phenotype-based classifier to the TCGA Lung Adenocarcinoma (LuAd) cohort and found that high MYC transcriptional activity identifies a subset of LuAd with significantly reduced survival. Application of the same methodology to a panel of genetically engineered mouse models identified multiple genotypes that give rise to the high MYC activity phenotype, disease positioning such models as reflective of a distinct subset of human LuAd. We show that high MYC activity predicts sensitivity to a small molecule dual-inhibitor of the MYC co-factors, EZH2 and G9A, HKMTi-1-005, and that treatment with HKMTi-1-005 strongly reduced MYC protein expression, induced B cell-mediated immune surveillance and suppressed growth of autochthonous KRasG12D-driven lung tumours. Statement of significanceThis work establishes the principle of indirectly targeting MYC in LuAd, via inhibition of associated enzymatic cofactors, EZH2 and G9A, and identifies a large subset of aggressive human LuAd with a high MYC activity signature that may benefit from this approach.

cancer biology↗

bioRxiv2026

A Closed Computational - Experimental Loop Identifies Metabolic Collapse at the Root of Macrophage Dysfunction due to Zinc Dyshomeostasis

Zinc plays a crucial role in immune regulation, the oxidative stress response, and epithelial barrier integrity, yet zincs precise role in regulating metabolic and immunological functions in myeloid cells remains poorly understood. Here, we employ a systems biology approach using constraint-based modeling to elucidate the consequences of myeloid-specific loss of ZIP8 on macrophage metabolic function and antibacterial capabilities. We demonstrate that macrophage populations in the lung of ZIP8 knockout (Zip8KO) mice exhibit widespread metabolic disruption, spanning glycolysis, butanoate metabolism, amino acid metabolism, and mitochondrial function. Specifically, Zip8KO macrophages exhibit impaired nutrient uptake and dysregulated energy metabolism, which is exacerbated following Streptococcus pneumoniae infection. Genome-scale metabolic modeling and flux analysis revealed a paradoxical pattern of metabolic suppression prior to infection, followed by overcompensation post-infection, potentially driving immune dysfunction. Consistent with these predictions Zip8KO bone marrow-derived macrophages displayed increased ATP demand and disrupted mitochondrial energetics, compromising their ability to control infection. Importantly, we identified succinate, and kynurenic acid as metabolites capable of restoring immune responses and validated their ability to enhance bacterial clearance in Zip8KO BMDMs. Together, these findings establish ZIP8 as a central regulator of immune-metabolic homeostasis and suggest potential therapeutic avenues to restore immune function in settings of zinc deficiency.

immunology↗

bioRxiv2025

Cell-specific RNA isoform remodeling in the aging mouse brain

Aging is associated with increases in risk of multiple chronic diseases and at the cellular level, with disruptions in RNA homeostasis. Single-cell transcriptomic studies have revealed RNA abundance heterogeneity across brain cell types but the more complex changes in RNA processing such as alternative splicing, isoform usage, transcription start and polyadenylation site selection remain uncharacterized. Here, we combine single-cell analysis with long-read nanopore sequencing to capture full-length RNA isoforms and uncover temporal changes in RNA transcription, processing, and alternative splicing in the aging mouse cortex and hippocampus. By profiling transcriptomes from young adult to very old mice, we identify non-linear, cell-type-specific isoform expression changes and isoform usage shifts, primarily driven by transcription start site selection. These aging-associated isoform changes alter the coding potential and poly(A) site position of genes. Our data also reveal a high proportion of senescence in immune cells, far exceeding that of other cell types. We also identify isoform markers that, when applied to a machine learning model, distinguish senescent from normal immune cells. This study provides a full-length RNA isoform-based atlas of the aging mouse brain, offering insights into RNA metabolism remodeling across brain cell types throughout the lifespan.

genomics↗

bioRxiv2025

METTL3 regulates exocytosis independently of m6A

RNA modification pathways are often mis-regulated in various cancers, with N6-methyladenosine (m6A) having a pivotal role in cancer progression and metastasis. Methyltransferase-like 3 (METTL3), a core component of the m6A methyltransferase complex, functions not only as an m6A writer but also promotes tumorigenesis through m6A-independent mechanisms. Here, we show that METTL3 is mislocalized to the cytoplasm in breast cancer tumors from patients, contributing to the oncogenic phenotype. Cytoplasmic METTL3 interacts with EXOC7, a key regulator of exocytosis, promoting its stabilization. Additionally, METTL3 regulates m6A-dependent alternative splicing of EXOC7. Silencing METTL3 impairs vesicle trafficking and the breast cancer secretome - effects that do not rely on its enzymatic activity but instead involve METTL3-mediated stabilization of EXOC7 and potentially other exocyst components. Furthermore, METTL3 knockdown impairs invadopodia formation, collagen matrix invasion, and focal adhesion morphology in vitro, while inhibition of METTL3 catalytic activity does not. Our findings uncover non-catalytic roles of METTL3 in regulating exocytosis and the cancer secretome.

molecular biology↗

bioRxiv2024

Pathway Thermodynamic Analysis Postulates Change in Glutamate Metabolism as a Key Factor in Modulating Immune Responses

BackgroundTemperature, as seen during fever, plays a pivotal role in modulating immune responses and maintaining cellular homeostasis. Shifts in temperature influence the thermodynamic feasibility of metabolic reactions, with Gibbs free energy ({Delta}G) serving as a key indicator of the spontaneity of reactions under specific conditions. By altering {Delta}G in response to temperature changes across various metabolite concentrations and cell types, we can gain insights into the thermodynamic properties of metabolic pathways and identify critical factors involved in metabolism and immune function. Using Max-Min Driving Force (MDF) analysis, we can assess changes in {Delta}G by varying temperature and metabolite concentrations, allowing for a detailed examination of thermodynamic feasibility at both the pathway and individual reaction levels. ResultsIn this study, MDF analysis is applied to measure the changes in the driving force of pathways and the {Delta}G of each reaction at normal human core temperature (310.15 K) and elevated temperatures (up to 315.15 K). Additionally, we explore how shifts in the thermodynamic feasibility of reactions under immune activation, compared to normal physiological conditions, highlight key metabolic intermediates--such as fructose-1,6-bisphosphate, glucose-6-phosphate, and several steps in glutamate metabolism--as important regulators of metabolic processes and immune responses. ConclusionThe goal of this study is to underscore the value of thermodynamic parameters such as {Delta}G, concentration, and temperature in identifying potential therapeutic targets, with the aim of mitigating the detrimental effects of fever while preserving its beneficial aspects.

immunology↗

bioRxiv2024

Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans

Pantoea agglomerans is one of four Pantoea species for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

microbiology↗

bioRxiv2024

Molecular profiling of frontal and occipital subcortical white matter hyperintensities in Alzheimer's disease

White matter hyperintensities (WMHs) are commonly detected on T2-weighted magnetic resonance imaging (MRI) scans, occurring in both typical aging and Alzheimers disease. Despite their frequent appearance and their association with cognitive decline, the molecular factors contributing to WMHs remain unclear. In this study, we investigated the transcriptomic profiles of two commonly affected brain regions with coincident AD pathology--frontal subcortical white matter (frontal-WM) and occipital subcortical white matter (occipital-WM)--and compared with age-matched healthy controls. Through RNA-sequencing in frontal- and occipital-WM bulk tissues, we identified an upregulation of genes associated with brain vasculature function in AD white matter. To further elucidate vasculature-specific transcriptomic features, we performed RNA-seq analysis on blood vessels isolated from these white matter regions, which revealed an upregulation of genes related to protein folding pathways. Finally, comparing gene expression profiles between AD individuals with high-versus low-WMH burden showed an increased expression of pathways associated with immune function. Taken together, our study characterizes the diverse molecular profiles of white matter changes in AD compared to normal aging and provides new mechanistic insights processes underlying AD-related WMHs.

neuroscience↗

bioRxiv2023

Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics

Quantification of the dynamics of RNA metabolism is essential for understanding gene regulation in health and disease. Existing methods rely on metabolic labeling of nascent RNAs and physical separation or inference of labeling through PCR-generated mutations, followed by short-read sequencing. However, these methods are limited in their ability to identify transient decay intermediates or co-analyze RNA decay with cis-regulatory elements of RNA stability such as poly(A) tail length and modification status, at single molecule resolution. Here we use 5-ethynyl uridine (5EU) to label nascent RNA followed by direct RNA sequencing with nanopores. We developed RNAkinet, a deep convolutional and recurrent neural network that processes the electrical signal produced by nanopore sequencing to identify 5EU-labeled nascent RNA molecules. RNAkinet demonstrates generalizability to distinct cell types and organisms and reproducibly quantifies RNA kinetic parameters allowing the combined interrogation of RNA metabolism and cis-acting RNA regulatory elements.

bioinformatics↗

bioRxiv2023

Dissecting Metabolic Landscape of Alveolar Macrophage

The highly plastic nature of Alveolar Macrophage (AM) plays a crucial role in the defense against inhaled particulates and pathogens in the lungs. Depending upon the signal, AM acquires either classically activated M1 phenotype or alternatively activated M2 phenotype. These phenotypes have specific functions and unique metabolic traits such as upregulated glycolysis and pentose phosphate pathway in M1 phase and enhanced oxidative phosphorylation and tricarboxylic acid cycle during M2 phase that help maintain the sterility of the lungs. In this study, we investigate the metabolic shift in the activated phases of AM (M1 and M2 phase) and highlight the roles of pathways other than the typical players of central carbon metabolism. Pathogenesis is a complex and elongated process where the heightened requirement for energy is matched by metabolic shifts that supplement immune response and maintain homeostasis. The first step of pathogenesis is fever; however, analyzing the role of physical parameters such as temperature is challenging. Here, we observe the effect of an increase in temperature on pathways such as glycolysis, pentose phosphate pathway, oxidative phosphorylation, tricarboxylic acid cycle, amino acid metabolism, and leukotriene metabolism. We report the role of temperature as a catalyst to the immune response of the cell. The activity of pathways such as pyruvate metabolism, arachidonic acid metabolism, chondroitin/heparan sulfate biosynthesis, and heparan sulfate degradation are found to be important driving forces in the M1/M2 phenotype. We have also identified a list of 34 reactions such as nitric oxide production from arginine and the conversion of glycogenin to UDP which play major roles in the metabolic models and prompt the shift of the M2 phenotype to M1 and vice versa. In future, these reactions could further be probed as major contributors in designing effective therapeutic targets against severe respiratory diseases. Author SummaryAlveolar macrophage (AM) is highly plastic in nature and has a wide range of functions including invasion/killing of bacteria to maintaining the homeostasis in the lungs. The regulatory mechanism involved in the alveolar macrophage polarization is essential to fight against severe respiratory conditions (pathogens and particulates). Over the years, experiments on mouse/rat models have been used to draw insightful inferences. However, recent advances have highlighted the lack of transmission from non-human models to successful in vivo human experiments. Hence using genome-scale metabolic (GSM) models to understand the unique metabolic traits of human alveolar macrophages and comprehend the complex metabolic underpinnings that govern the polarization can lead to novel therapeutic strategies. The GSM models of AMs thus far, has not incorporated the activated phases of AM. Here, we aim to exhaustively dissect the metabolic landscape and capabilities of AM in its healthy and activated stages. We carefully explore the changes in reaction fluxes under each of the conditions to understand the role and function of all the pathways with special attention to pathways away from central carbon metabolism. Understanding the characteristics of each phase of AM has applications that could help improve the therapeutic approaches against respiratory conditions.

systems biology↗

bioRxiv2023

Full-length direct RNA sequencing reveals widespread RNA decay upon cellular stress

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5 end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5 end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.

cell biology↗

bioRxiv2023

Fish on the platter! Investigating the dietary habits of fishing cats (Prionailurus viverrinus) in the Godavari Delta, India

The threatened fishing cat (Prionailurus viverrinus) is an elusive and medium-sized cat that is adapted to mangroves, swamps, wetlands, and riverine habitats. A close look at the literature indicates that fishing cats are piscivorous, however this is based on very few studies. Understanding the patterns of resource utilisation by species is crucial for assessing their role in ecosystems and in ensuring their conservation. Therefore, our study presents insights into fishing cat feeding patterns from mangroves of the Godavari delta, Andhra Pradesh, India. We collected 303 putative fishing cat scats and conducted analysis using 120 genetically identified scats. Our analysis revealed that fish was the most important prey by fishing cats in the study area, followed by crabs and rodents. The prey composition did not vary significantly between the three seasons but there were differences between the survey years. The niche breadth also varied across the three seasons, from being a generalist in winters to a specialist in summers. Our results suggest that long term conservation and survival of the fishing cats depends on fish populations, which are the main prey of the species and thus recommend the need to protect the fish populations in the Godavari delta and the surrounding riverine habitats. Given the importance of fish to the diet of the fishing cat, the health of waterways throughout their distribution must be one of the focal strategies of conservation action.

ecology↗

bioRxiv2023

The catalytic-independent function of LSD1 modulates the epigenetic landscape of mouse embryonic stem cells

Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di-methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for embryonic stem cell (ESC) self-renewal but is required for ESC growth and differentiation. Reexpression of a catalytically-dead LSD1 (LSD1MUT) recovers the proliferation capability of ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, a gain of H3K4me1 in Lsd1 knockout (KO) ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUT results in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUT control protein stability of UHRF1 and DNMT1 through interaction with the ubiquitin-specific peptidase 7 (USP7) and, consequently, inhibiting DNMT1 and UHRF1 ubiquitylation. Our studies elucidate for the first time a novel mechanism by which the scaffolding function of LSD1 controls DNA methylation in ESCs.

molecular biology↗

bioRxiv2023

Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens

Drug targets with human genetic evidence are expected to increase clinical success by at least two-fold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge of early drug discovery. A key issue is that, currently, the vast majority of complex disease associations cannot be cleanly mapped to a gene. Immune disease-associated variants are enriched within regulatory elements, such as distal enhancers, found in T cell-specific open chromatin regions. To identify the genes and thus the molecular programs modulated by these regulatory elements, we developed a CRISPRi-based single-cell functional screening approach in primary human CD4+ T cells. Our pipeline enables the interrogation of transcriptomic changes induced by the perturbation of regulatory elements at scale. We first optimised a highly efficient CRISPRi protocol in primary human CD4+ T cells via CROPseq vectors. Subsequently, we performed a proof-of-concept screen targeting 45 non-coding regulatory elements and 35 transcription start sites and profiled approximately 250,000 CD4+ T cell single-cell transcriptomes. We developed a bespoke analytical pipeline for element-to-gene (E2G) mapping and demonstrate that our method can identify both previously annotated and novel E2G links. Lastly, we integrated genetic association data for immune-related traits and demonstrate how our platform can aid in the identification of effector genes for GWAS loci.

genomics↗

bioRxiv2023

Transient expression of Helicobacter pylori cagA oncoprotein in brinjal

Helicobacter pylori is closely connected to upper gastrointestinal tract diseases including gastric cancer. Transgenic plants are found to be successful in expressing the bacterial antigens, which could elicit an immune response when consumed. The Cytotoxicity-associated immunodominant antigen protein (cagA) of H. pylori is kindred with pathogenicity and cancer risk. We expressed the cagA transgenically in the brinjal. We amplified the cagA gene from H. pylori strain 26695 chromosomal DNA and transformed it into brinjal callus derived from leaf explants using the pBI121 expression vector. The stable expression and accumulation of the recombinant cagA gene were confirmed by using quantitative real-time PCR, western blot analysis and ELISA. The RT-PCR, western blot and ELISA showed stable expression of cagA gene in the transgenic lines B3, B5, B11, B17 and B21. Among them, B11 and B17 samples showed higher expression of the cagA compared to the other samples. Besides, the immunohistochemistry assay showed the abundant expression of cagA protein in the parenchymal regions of the transgenic plants. Out of the 52 plants, a set five plants were found to be positive for cagA expression. Our experimental outcomes can be used further to design the vaccines against H. pylori from the transgenic brinjal plants.

molecular biology↗

bioRxiv2023

Senescence-specific translation dysregulation desensitizes cells to stress by inhibiting activation of the integrated stress response

Senescence is a state of indefinite cell cycle arrest associated with aging, cancer, and age-related diseases. Here, using label-based mass spectrometry, ribosome profiling and nanopore direct RNA sequencing, we explore the coordinated interaction of translational and transcriptional programs of human cellular senescence. We find that translational deregulation and a corresponding maladaptive integrated stress response (ISR) is a hallmark of senescence that desensitizes senescent cells to stress. We present evidence that senescent cells maintain high levels of eIF2 phosphorylation, typical of ISR activation, but translationally repress production of the stress response transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames. Surprisingly, ATF4 translation remains inhibited even after acute proteotoxic and amino acid starvation stressors, resulting in a highly diminished stress response. Furthermore, absent a response, stress augments the senescence secretory phenotype, thus intensifying a proinflammatory state that exacerbates disease. Our results reveal a novel mechanism that senescent cells exploit to evade an adaptive stress response and remain viable.

molecular biology↗

bioRxiv2022

MmCMS: Mouse models' Consensus Molecular Subtypes of colorectal cancer

BACKGROUNDColorectal cancer (CRC) primary tumours are molecularly classified into four consensus molecular subtypes (CMS1-4). Genetically engineered mouse models aim to faithfully mimic the complexity of human cancers and, when appropriately aligned, represent ideal pre-clinical systems to test new drug treatments. Despite its importance, dual-species classification has been limited by the lack of a reliable approach. Here we utilise, develop and test a set of options for human-to-mouse CMS classifications of CRC tissue. METHODSUsing transcriptional data from established collections of CRC tumours, including human (TCGA cohort; n=577) and mouse (n=57 across n=8 genotypes) tumours with combinations of random forest and nearest template prediction algorithms, alongside gene ontology collections, we comprehensively assess the performance of a suite of new dual-species classifiers. RESULTSWe developed three approaches: MmCMS-A; a gene-level classifier, MmCMS-B; an ontology-level approach and MmCMS-C; a combined pathway system encompassing multiple biological and histological signalling cascades. Although all options could identify tumours associated with stromal-rich CMS4-like biology, MmCMS-A was unable to accurately classify the biology underpinning epithelial-like subtypes (CMS2/3) in mouse tumours. CONCLUSIONSWhen applying human-based transcriptional classifiers to mouse tumour data, a pathway-level classifier, rather than an individual gene-level system, is optimal. Our R package with three options helps researchers select suitable mouse models of human CRC subtype for their experimental testing.

cancer biology↗