Biology subjects

Shah, M. A.

Publications and source records attributed to Shah, M. A..

8 recordsLinked to original sources

bioRxiv2026

A Foundation Model for the Cancer Genome

AO_SCPLOWBSTRACTC_SCPLOWCancer is a disease of the genome, in which somatic mutations and copy-number alterations determine tumour identity, clinical behaviour, and response to therapy. Consortium-scale sequencing has profiled hundreds of thousands of tumours,1,2 yet clinical interpretation still proceeds one alteration at a time against hand-curated knowledgebases,3,4 often ignoring co-occurring alterations and the genome-wide copy-number pattern. Self-supervised foundation models pretrained on unlabelled corpora5 have produced transferable representations in adjacent biological domains6-8 by learning joint structure across many features, yet no comparable model exists for the cancer genome. Here we present TESSERA (Tumour Embeddings via Self-Supervised Encoding and Reconstruction of Alterations), a foundation model for the cancer genome; we pretrain it on somatic single-nucleotide variants and copy-number segments through masked-token reconstruction within each modality and a contrastive objective across modalities. A single representation, produced once and reused without retraining, supports variant pathogenicity prediction, pan-cancer tumour typing, unsupervised molecular subtyping, prognostic stratification, and counterfactual treatment-effect estimation that yields predictive chemotherapy-selection biomarkers in real-world cohorts. These biomarkers are interpretable: each surfaces the co-occurring alterations underlying the prediction, exposing biology that single-gene rules miss. In metastatic colorectal cancer, where the FOLFOX-vs-FOLFIRI choice is currently guided by toxicity rather than tumour biology, the model uncovers a candidate predictive biomarker: a three-feature rule (TP53+/KRAS+/17p-) selecting patients who derive substantially greater benefit from FOLFOX than FOLFIRI.

bioinformatics↗

bioRxiv2025

Targeted ablation and regeneration of enteric nervous system neurons in zebrafish

The enteric nervous system (ENS) is the intrinsic nervous system of the gut and regulates essential gut functions, including motility, digestion, and immune response, ensuring gut homeostasis. ENS dysfunction or loss is associated with gastrointestinal disorders such as Hirschsprung disease (HSCR). Currently, surgery is the only treatment for HSCR, but it often has lifelong, severe complications. Restoring missing ENS neurons by stimulating endogenous neuronal regeneration presents a promising therapeutic approach for ENS disease. To reveal the cellular-molecular mechanisms regulating neuronal regeneration we study a species capable of robust ENS restoration, the zebrafish. For this, we developed a chemogenetic ablation model in zebrafish using the Gal4/UAS NTR 2.0 system for targeted ENS neuron ablation. Spatially and temporally controlled neuronal death was confirmed by morphological changes, quantification of neuronal loss, and TUNEL assays. We observed an acute immune response that normalizes at 1 day of treatment. Quantification of regenerated neurons demonstrated complete restoration of ENS neuron numbers to control levels by 9 days post treatment, with recovery of gut motility. Among the regenerated neurons, nitrergic, cholinergic and VIPergic subtypes showed full recovery, whereas serotonergic neurons only displayed partial recovery, indicating subtype-specific differences in regenerative capacity and/or timing of cell replacement. Our study establishes a robust platform for dissecting the cellular-molecular mechanisms of ENS regeneration to develop potential treatment approaches for ENS-related diseases.

neuroscience↗

bioRxiv2025

The role of lipoteichoic acid in Staphylococcus aureus cell wall integrity

In Staphylococcus aureus, lipoteichoic acid (LTA) is crucial for growth, cell division, osmoprotection, and beta-lactam resistance, yet its molecular mechanisms remain unclear. This study reveals that LTA binds to multiple proteins involved in cell wall processes and preserves cell wall integrity by regulating one of the LTA-binding proteins, ScaH. ScaH is a peptidoglycan hydrolase predicted to have N-acetylglucosaminidase and amidase/peptidase activities. LTA inhibits ScaHs enzymatic activities by direct binding and represses scaH transcription by an unknown mechanism. During early growth, LTA is highly expressed and sequesters ScaH at the cell membrane, preventing ScaH activity in the cell wall. However, LTA expression decreases during the late growth phase, leading to ScaH translocation into the cell wall. This reduction in LTA coincides with increased wall teichoic acid (WTA) expression and cleavage of the LTA synthase LtaS. In the LTA-null mutant, ScaH inactivation restored peptidoglycan crosslinking, osmoresistance, and beta-lactam resistance both in vitro and in vivo. These findings suggest that LTA protects the cell wall by suppressing ScaH expression and activity while sequestering it during active growth. Additionally, the reciprocal expression patterns of LTA and WTA indicate an interconnected regulation of teichoic acids in S. aureus, with their roles likely depending on the growth phase. ImportanceStaphylococcus aureus is a significant human pathogen, with LTA playing a crucial role in cell viability, division, and maintaining cell wall integrity. Targeting LTA synthesis holds promise for the development of new therapeutics against S. aureus. Disruption of LTA synthesis leads to phenotypes indicative of compromised cell wall integrity, such as reduced crosslinking, osmosensitivity, and heightened beta-lactam sensitivity, although the precise underlying mechanisms remain unclear. Our research demonstrates that LTA contributes to cell wall integrity by regulating the expression, activity, and translocation of the peptidoglycan hydrolase ScaH. Additionally, LTAs binding to the cell wall synthesis enzymes suggests a role in modulating cell wall integrity through these interactions. These findings significantly advance our understanding of LTAs physiological functions and may serve as a foundation for the development of novel therapeutics targeting S. aureus and other Gram-positive pathogens.

microbiology↗

bioRxiv2024

Darwin's Naturalization Conundrum explained by gradients of environmental stress and disturbance

Darwins Naturalization Conundrum (DNC) states that non-native species closely related to the native community are either more likely to succeed because shared adaptations help them overcome environmental filtering, or less likely to succeed because of strong competition with their native relatives. Despite extensive research, no general patterns have so far emerged. One reason may be that the relative importance of competition and environmental filtering depends on environmental conditions. To test this hypothesis, we conducted a global assessment of DNC examining patterns of phylogenetic relatedness of non-native plant species to the native community along gradients of elevation and anthropogenic disturbance in mountains. Phylogenetic distance of non-native to native species decreased with increasing elevation and in disturbed plant communities. Our results help resolve DNC by showing that the environmental context sets expectations for patterns of relatedness between non-native and native species and helps illuminate the ecological and evolutionary processes generating these patterns.

ecology↗

bioRxiv2023

Clinal variation in drought response is consistent across life stages but not between native and non-native ranges

Clinal variation, i.e., intraspecific variation that corresponds to environmental gradients, is common in widely distributed species. Studies on clinal variation across multiple ranges and life stages are lacking, but can enhance our understanding of specie[s] adaptive potential to abiotic environments and may aid in predicting future species distributions. This study examined clinal variation in drought responses of 59 Conyza canadensis populations across large aridity gradients from the native and non-native ranges in three greenhouse studies. Experimental drought was applied to recruitment, juveniles, and adult stages. Drought reduced growth at all three life stages. However, contrasting patterns of clinal variation emerged between the two ranges. Native populations from xeric habitats were less inhibited by drought than mesic populations, but such clinal variation was not apparent for non-native populations. These range-specific patterns of clinal variation were consistent across the life stages. The experiments suggest that invaders may succeed without complete local adaptation to their new abiotic environments, and that long-established invaders may still be evolving to the abiotic environment. These findings may explain lag times in some invasions and raise concern about future expansions.

evolutionary biology↗

bioRxiv2022

Staphylococcus aureus does not synthesize arginine from proline under physiological conditions

The Gram-positive pathogen Staphylococcus aureus is the only bacterium known to synthesize arginine from proline via the arginine-proline interconversion pathway, despite having genes for the well-conserved glutamate pathway. Since the proline-arginine interconversion pathway is repressed by CcpA-mediated carbon catabolite repression (CCR), CCR has been attributed to the arginine auxotrophy of S. aureus. Using ribose as a secondary carbon source, here, we demonstrate that S. aureus arginine auxotrophy is not due to CCR but due to the inadequate concentration of proline degradation product. Proline is degraded by proline dehydrogenase (PutA) into pyrroline-5-carboxylate (P5C). Although the PutA expression was fully induced by ribose, the P5C concentration remained insufficient to support arginine synthesis because P5C was constantly consumed by the P5C reductase ProC. When the P5C concentration was artificially increased by either PutA overexpression or proC-deletion, S. aureus could synthesize arginine from proline regardless of carbon source. In contrast, when the P5C concentration was reduced by overexpression of proC, it inhibited the growth of the ccpA-deletion mutant without arginine. Intriguingly, the ectopic expression of the glutamate pathway enzymes converted S. aureus into arginine prototroph. In an animal experiment, the arginine-proline interconversion pathway was not required for the survival of S. aureus. Based on these results, we concluded that S. aureus does not synthesize arginine from proline under physiological conditions. We also propose that arginine auxotrophy of S. aureus is not due to the CcpA-mediated CCR but due to the inactivity of the conserved glutamate pathway. ImportanceStaphylococcus aureus is a versatile Gram-positive human pathogen infecting various human organs. The bacteriums versatility is partly due to efficient metabolic regulation via the carbon catabolite repression system (CCR). S. aureus is known to interconvert proline and arginine, and CCR represses the synthesis of both amino acids. However, when CCR is released by a non-preferred carbon source, S. aureus can synthesize proline but not arginine. In this study, we show that, in S. aureus, the intracellular concentration of pyrroline-5-carboxylate (P5C), the degradation product of proline and the substrate of proline synthesis, is too low to synthesize arginine from proline. These results call into question the notion that S. aureus synthesizes arginine from proline.

microbiology↗

bioRxiv2021

Who is the best surrogate for germ stem cell transplantation in fish?

Surrogate reproduction technology in fish has potential for aquaculture as well as endangered species preservation and propagation. Species with some unfavourable biological characteristics for culturing such as a late maturation or a large body size are ideal candidates for surrogate reproduction using smaller and faster-maturing host. One of the general prerequisites for the successful surrogacy and the pure donor-derived gamete production is the sterility of the host. Various sterilization methods have been developed and used in fish surrogacy; however, a direct comparison of available methods is missing. Such a knowledge gap hinders choice for the surrogate in various fish species, including those in high commercial demand such as tuna or sturgeons, where is a particular limitation from the point of the live material availability and difficulty to perform a high throughput assessment of different surrogates. Yet, large sturgeons or tuna species are one of the most prominent candidates for surrogacy. Zebrafish was utilized in this study as a model species to answer whether and to which extent different sterilization strategies can affect the surrogacy. Germ cell-depleted recipients (produced using knockdown of dead end gene), triploid recipients, and zebrafish x pearl danio hybrid recipients were tested as they represent the most frequently used types of surrogates. Spermatogonia isolated from vas::EGFP transgenic strain were intraperitoneally transplanted into swim-up 5-day old zebrafish. Transplantation success, survival, gonadal development, and reproductive output of the fish was analyzed. Germ cell-depleted recipients with empty gonads were identified as the most convenient among tested sterilization methods considering surrogacy induction success and reproductive output. The present study stands as significant aid for selecting suitable surrogates in various fish species.

cell biology↗

bioRxiv2019

Imatinib overrides taxane resistance by selective inhibition of novel CLIP1 variant obstructing the microtubule pore

Despite its widespread use, the majority of patients with gastric cancer (GC) will not respond to taxane chemotherapy due to resistance mechanisms. Here, we report the discovery of a novel truncated variant of the microtubule plus-end binding protein (+TIP) CLIP-170, hereafter CLIP-170S, whose expression is enriched in taxane resistant cell lines and patients with GC. To establish causation, we knocked-down (KD) CLIP-170S which completely reversed taxane resistance. Mass-spec proteomics and 5-RACE further showed that CLIP-170S lacked the first 150 amino acids, including the Cap-Gly motif required for microtubule (MT) plus-end localization. Mechanistically, we show that CLIP-170S was mislocalized from the MT plus-end to the MT lattice obstructing the MT pore surface site required for taxane entry into the MT lumen. Computational analysis of RNA-seq data from taxane-sensitive and resistant GC cell lines, predicted imatinib as the top candidate drug to overcome drug resistance. Imatinib treatment completely reversed taxane resistance, as predicted, and did so unexpectedly by selective depletion of CLIP-170S. Importantly, CLIP170S was found to be highly prevalent in tumor biopsies from patients with GC. Taken together, these data identify CLIP-170S as a novel, clinically prevalent +TIP variant that obstructs the MT pore and confers taxane resistance. The discovery of this previously unrecognized variant together with the computational discovery of Imatinib as a selective CLIP-170S inhibitor, implicate the MT pore in clinical taxane resistance and provide new therapeutic opportunities for treatment of GC and beyond.

cancer biology↗