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Matar, S.

Publications and source records attributed to Matar, S..

5 recordsLinked to original sources

CRISPR/Cas9 gene editing in the heterotrophic protist Acanthamoeba castellanii

Members of the amoebozoan genus Acanthamoeba are unicellular heterotrophic protists that inhabit a wide range of terrestrial and aquatic environments. They are opportunistic pathogens known to host disease-causing bacteria as well large DNA viruses. While Acanthamoeba is commonly used to study cellular locomotion, phagocytosis, and disease, genetic tools for precise editing of the Acanthamoeba genome are still in their infancy. Here we have developed CRISPR/Cas9 tools for genetically engineering the model acanthamoebid Acanthamoeba castellanii strain Neff. In proof-of-principle experiments, we targeted the myosin-II heavy chain gene. Evidence for editing was found using reverse transcriptase PCR, microscopy, and DNA sequencing, which also identified unique alleles for the target locus. Collectively, we demonstrate that CRISPR can be employed to edit Acanthamoeba genes using a knock-in approach. This work serves as a foundation to further develop A. castellanii as a model system with which to study diverse questions in cell and molecular biology, biochemistry and evolution.

molecular biology↗

Fusion-driven oncogenic programs shape the immune landscape in translocation renal cell carcinoma

Renal cell carcinomas comprise multiple molecularly distinct cancers but most are treated empirically with therapies designed for clear cell RCC (ccRCC), the most common subtype, due to incomplete understanding of subtype-specific biology. We analyzed single-cell transcriptomes and chromatin accessibility profiles from translocation renal cell carcinoma (tRCC), an aggressive RCC defined by oncogenic TFE3 gene fusions. Unexpectedly, despite arising from a proximal tubule cell of origin similar to ccRCC, tRCCs display markedly distinct oncogenic programs and an immunosuppressive tumor microenvironment. tRCCs exhibit six conserved tumor meta-programs, including epithelial-mesenchymal transition and proximal tubule identity programs whose balance is regulated by TFE3 fusion activity. The fusion-driven EMT program drives a suppressive TME marked by progenitor-exhausted CD8+ T cells, anti-inflammatory SPP1+ macrophages, and matrix-associated fibroblasts (mCAFs). Our findings highlight unique TFE3 fusion-driven biology in tRCC, explaining its reduced immunotherapy responsiveness relative to ccRCC, and suggesting strategies for targeting fusion-driven oncogenic programs and TME reprogramming.

genomics↗

Neural bases of proactive and predictive processing of meaningful sub-word units in speech comprehension

To comprehend speech, human brains identify meaningful units in the speech stream. But whereas the English She believed him. has 3 words, the Arabic equivalent saddaqathu. is a single word with 3 meaningful sub-word units, called morphemes: a verb stem ( saddaqa), a subject suffix ( -t-), and a direct object pronoun ( -hu). It remains unclear whether and how the brain processes morphemes, above and beyond other language units, during speech comprehension. Here, we propose and test hierarchically-nested encoding models of speech comprehension: a NAIVE model with word-, syllable-, and sound-level information; a BOTTOM-UP model with additional morpheme boundary information; and PREDICTIVE models that process morphemes before these boundaries. We recorded magnetoencephalography (MEG) data as participants listened to Arabic sentences like saddaqathu.. A temporal response function (TRF) analysis revealed that in temporal and left inferior frontal regions PREDICTIVE models outperform the BOTTOM-UP model, which outperforms the NAIVE model. Moreover, verb stems were either length-AMBIGUOUS (e.g., saddaqa could initially be mistaken for the shorter stem sadda= blocked) or length-UNAMBIGUOUS (e.g., qayyama= evaluated cannot be mistaken for a shorter stem), but shared a uniqueness point, at which stem identity is fully disambiguated. Evoked analyses revealed differences between conditions before the uniqueness point, suggesting that, rather than await disambiguation, the brain employs PROACTIVE PREDICTIVE strategies, processing the accumulated input as soon as any possible stem is identifiable, even if not unique. These findings highlight the role of morpheme processing in speech comprehension, and the importance of including morpheme-level information in neural and computational models of speech comprehension. Significance statementMany leading models of speech comprehension include information about words, syllables and sounds. But languages vary considerably in the amount of meaning packed into word units. This work proposes speech comprehension models with information about meaningful sub-word units, called morphemes (e.g., bake- and -ing in baking), and shows that they explain significantly more neural activity than models without morpheme information. We also show how the brain predictively processes morphemic information. These findings highlight the role of morphemes in speech comprehension and emphasize the contributions of morpheme-level information-theoretic metrics, like surprisal and entropy. Our models can be used to update current neural, cognitive, and computational models of speech comprehension, and constitute a step towards refining those models for naturalistic, connected speech.

neuroscience↗

Epigenomic signatures as circulating and predictive biomarkers in sarcomatoid renal cell carcinoma

Renal cell carcinoma with sarcomatoid differentiation (sRCC) is associated with poor survival and heightened response to immune checkpoint inhibitors (ICIs). Two major barriers to improving outcomes for sRCC are (1) a limited understanding of its gene regulatory programs and (2) difficulty identifying sarcomatoid differentiation on tumor biopsies due to spatial heterogeneity. To address these challenges, we characterized the epigenomic landscape of sRCC by profiling 107 epigenomic libraries in tissue and plasma samples from 50 patients with RCC and healthy volunteers. We identified highly recurrent epigenomic reprogramming, as assessed by histone modifications and DNA methylation, that distinguishes sRCC from non-sarcomatoid RCC. Computational analysis of RCC epigenomic profiles and CRISPRa experiments implicated the transcription factor FOSL1 in activating sRCC-associated gene regulatory programs. Analysis of two randomized clinical trials identified FOSL1 expression as a predictive biomarker of response to ICIs in RCC. Finally, we demonstrate that epigenomic signatures of sRCC are detectable in patient plasma, establishing an approach for blood-based diagnosis of this clinically important phenotype. These findings provide a framework for the discovery and non-invasive detection of epigenomic correlates of tumor histology via liquid biopsy.

genomics↗

The SLC1A1/EAAT3 Dicarboxylic Amino Acid Transporter is an Epigenetically Dysregulated Nutrient Carrier that Sustains Oncogenic Metabolic Programs

Inactivation of pVHL tumor suppressor in clear cell Renal Cell Carcinoma (ccRCC) increases the abundance of Histone H3 lysine 27 acetylation (H3K27ac). We hypothesized that H3K27ac, a marker of transcriptional activation, drives the expression of critical oncogenes in ccRCC. Using H3K27ac ChIP-Seq; RNA-Seq; an in vivo positive selection screen; cell-based functional studies; and clinical validations; here, we report the identification of the SLC1A1/EAAT3 aspartate (Asp) and glutamate (Glu) transporter as a ccRCC oncogene. pVHL loss promotes SLC1A1 expression in a HIF-independent manner. Importantly, SLC1A1 inactivation depletes Asp/Glu-derived metabolites, impedes ccRCC growth both in vitro and in vivo, and sensitizes ccRCCs to metabolic therapeutics (e.g., glutaminase blockers). Finally, in human ccRCC biospecimens, higher SLC1A1 expression is associated with metastatic disease and clusters with elevated expression of other solute carriers, but not HIF/Hypoxia pathways. Altogether, our studies identify a HIF-independent metabolic hub in ccRCC and credential SLC1A1 as an actionable ccRCC oncogene. STATEMENT OF SIGNIFICANCETargeting chronic HIF activation underlies many therapeutic strategies in ccRCC; but, unfortunately, is not curative. SLC1A1, instead, represents a HIF-independent ccRCC dependency, which is targetable alone and together with other antimetabolites, such as glutaminase inhibitors. These observations identify an actionable metabolic program that functions independent of HIF in ccRCC.

cancer biology↗