Biology subjects

Kamal, M.

Publications and source records attributed to Kamal, M..

17 recordsLinked to original sources

bioRxiv2026

The Nematicide Tioxazafen Disrupts Proteasome Function via Cytochrome P450 Bioactivation

Tioxazafen is an effective nematicide whose commercialization was halted because handlers reportedly developed rashes after working with seeds coated with a tioxazafen-laced cocktail. Here, we show that tioxazafen is bioactivated into toxic products by nematode and human cytochrome P450s. Through systematic analyses, we found that bioactivated tioxazafen disrupts proteasome function, leading to the accumulation of the NRF1 transcription factor ortholog SKN-1A in the nematode C. elegans, and a bounce-back transcriptional up-regulation of proteasome components. Genetic upregulation of the C. elegans proteasome supresses tioxazafens lethality, indicating that proteotoxicity is a key contributor to death. A survey of human P450s revealed that skin-expressed CYP1A1 toxifies tioxazafen and may account for the reaction to tioxazafen-coated seeds. We also found that rabbit CYP1A1 fails to bioactivate tioxazafen, which may explain the pre-market failure to detect robust adverse skin reactions. Our work highlights vulnerabilities in pre-market toxicological assays and a provides potential solution to prospectively identifying P450 toxication events. One-Sentence SummaryTioxazafen is bioactivated by cytochrome P450s into a proteasome disruptor.

pharmacology and toxicology↗

bioRxiv2026

Single-cell trajectories in metastatic urothelial carcinoma reveal tumor-immune reprogramming and macrophage-driven resistance to PD-(L)1 blockade

Immune checkpoint inhibitors (ICI) improved outcomes in metastatic urothelial carcinoma (mUC), but primary and acquired resistance remain poorly understood. We performed single-nuclei RNA sequencing on sequential metastatic biopsies from ICI-treated mUC patients. Tumor cells showed transcriptomic heterogeneity within individual lesions, basal cells being associated with increased immune infiltration and response. Myeloid and lymphoid compartments exhibited features of immune dysfunction in non-responders. Longitudinal analyses revealed convergent adaptive resistance mechanisms, dominated by polarization toward pro-tumoral macrophage states, but also including downregulation of the antigen presentation machinery in tumor cells, increased checkpoint expression with loss of cytotoxicity in T cells. Individual trajectories point to distinct evolutionary routes under ICI pressure. Across pivotal ICI trials, bulk expression of the M2-like macrophage marker HES1 predicted ICI resistance. Our study provides the first single-cell longitudinal atlas of ICI-treated mUC, revealing macrophage reprogramming as a dominant driver of resistance, establishing a framework for individualized immunotherapy strategies.

cancer biology↗

bioRxiv2025

A single-nucleus multimodal framework reveals epigenomic priming of chemoresistant states in ovarian cancer

Non-genetic intratumor heterogeneity (ITH) drives therapeutic failure in cancer, yet its clinical monitoring remains challenging. We develop a multimodal single-nucleus framework that simultaneously profiles transcriptional and histone modification landscapes from frozen biopsies. Applied to longitudinal samples from 16 patients with high-grade serous ovarian cancer (HGSOC), this approach reveals reproducible tumor evolution under chemotherapy: proliferative and interferon-responsive states are lost, while those associated with TNF- and epithelial-mesenchymal transition (EMT) expand. Chromatin profiling shows that these chemoresistant programs are epigenetically primed through H3K4me1 marks before treatment and nominates transcription-factor drivers, including ZBTB7A. Non-genetic baseline tumor composition predicts survival, and fibroblast remodeling parallels malignant adaptation. These findings establish a clinically scalable strategy for mapping functional ITH and identify epigenomic priming as a determinant of therapeutic failure. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=181 HEIGHT=200 SRC="FIGDIR/small/692102v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@432524org.highwire.dtl.DTLVardef@3b7843org.highwire.dtl.DTLVardef@54a2eforg.highwire.dtl.DTLVardef@95273d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples

Viruses are a leading cause of human morbidity and mortality. Certain viruses, including human papillomaviruses (HPVs), play a significant role in the etiology of cancer. Detection of viral DNA insertions in the human genome from next generation sequencing data defines viral associations with cancer and other diseases, identifies impacted organs and tissues, provides insights into disease mechanisms and has the potential to enhance clinical evaluations. In this study, we developed VirusIntegrationFinder (CTAT-VIF), a tool for surveying human genome insertions of various human viruses using both DNA and RNA sequencing data. We applied CTAT-VIF to analyze a dataset of over 30,000 tumor and normal samples, as well as more than 1,000 cancer cell lines. This effort resulted in the compilation of a catalog of over 30,0000 virus-human DNA or RNA junctions at more than 20,000 insertion loci and reassessed viral cancer-insertion hotspots across the human genome. Furthermore, we characterized the functional impacts of insertions with respect to human copy number alterations, effects on the expression of flanking human genes, and the identification of potentially oncogenic chimeric human and human/virus fusion transcripts at insertion loci. In addition to confirming known viral associations with specific tumor types, our study revealed both shared and virus-specific insertion hotspots in addition to variable functional impacts based on virus type. Besides some rare events of interest, we also found evidence for sequencing contamination, which underscores the need for vigilance when studying viral content or genome integrations.

cancer biology↗

bioRxiv2024

Polyploid cancer cells reveal signatures of chemotherapy resistance

Therapeutic resistance in cancer significantly contributes to mortality, with many patients eventually experiencing recurrence after initial treatment responses. Recent studies have identified therapy-resistant large polyploid cancer cells in patient tissues, particularly in late-stage prostate cancer, linking them to advanced disease and relapse. Here, we analyzed bone marrow aspirates from 44 advanced prostate cancer patients and found the presence of circulating tumor cells with increased genomic content (CTC-IGC) was significantly associated with poorer progression- free survival. Single cell copy number profiling of CTC-IGC displayed clonal origins with typical CTCs, suggesting complete polyploidization. Induced polyploid cancer cells from PC3 and MDA-MB-231 cell lines treated with docetaxel or cisplatin were examined through single cell DNA sequencing, RNA sequencing, and protein immunofluorescence. Novel RNA and protein markers, including HOMER1, TNFRSF9, and LRP1, were identified as linked to chemotherapy resistance. These markers were also present in a subset of patient CTCs and associated with recurrence in public gene expression data. This study highlights the prognostic significance of large polyploid tumor cells, their role in chemotherapy resistance, and their expression of markers tied to cancer relapse, offering new potential avenues for therapeutic development.

cancer biology↗

bioRxiv2023

MET functions in tumour progression and therapy resistance are repressed by intronic polyadenylation

Intronic polyadenylation (IPA) leads to the production of transcript isoforms with alternative last exons in thousands of mammalian genes. Widespread regulation of IPA isoforms was observed during oncogenic transformation and in tumours versus healthy tissues, and several IPA isoforms were involved in oncogenesis. However, little is known about the potential involvement of IPA in tumour progression, such as cancer cell invasiveness and metastasis, and in resistance to anticancer therapies. Here, we show that an IPA isoform of MET (short MET) whose production is inhibited by U1 snRNP (U1), an essential ribonucleoprotein complex that recognizes the 5 exon-intron junction of pre-mRNA, is associated with better prognosis in breast cancer. Induction of the short MET isoform, using a steric-blocking antisense oligonucleotide targeting the U1 binding site in the vicinity of the short MET alternative polyadenylation site, antagonizes cell invasiveness. U1 blockade with an antisense oligonucleotide targeting the U1 snRNA also decreases breast cancer cell invasiveness, in both human and mouse cancer cell models, and this effect involves IPA induction in MET and several genes belonging to the RAS/RAF/MAPK signalling pathway. Finally, short MET relieves melanoma cell resistance to MAPK cascade-targeted therapy in vitro and in vivo. IPA isoform levels of MET and a few other genes (mTOR, EGFR and CTNNA1) help predict such resistance in patients. Altogether, our findings provide evidence for a role of IPA in both cancer cell invasiveness and resistance to therapy. This suggests that IPA isoforms can be exploited as biomarkers and therapeutic targets to combat tumour progression.

molecular biology↗

bioRxiv2023

Metabolic benefits of 17α-estradiol in liver are partially mediated by ERβ in male mice

Metabolic dysfunction underlies several chronic diseases. Dietary interventions can reverse metabolic declines and slow aging but remaining compliant is difficult. 17-estradiol (17-E2) treatment improves metabolic parameters and slows aging in male mice without inducing significant feminization. We recently reported that estrogen receptor is required for the majority of 17-E2-mediated benefits in male mice, but that 17-E2 also attenuates fibrogenesis in liver, which is regulated by estrogen receptor {beta} (ER{beta})-expressing hepatic stellate cells (HSC). The current studies sought to determine if 17-E2-mediated benefits on systemic and hepatic metabolism are ER{beta}-dependent. We found that 17-E2 treatment reversed obesity and related systemic metabolic sequela in both male and female mice, but this was partially blocked in female, but not male, ER{beta}KO mice. ER{beta} ablation in male mice attenuated 17-E2-mediated benefits on hepatic stearoyl-coenyzme A desaturase 1 (SCD1) and transforming growth factor {beta}1 (TGF-{beta}1) production, which play critical roles in HSC activation and liver fibrosis. We also found that 17-E2 treatment suppresses SCD1 production in cultured hepatocytes and hepatic stellate cells, indicating that 17-E2 directly signals in both cell-types to suppress drivers of steatosis and fibrosis. We conclude that ER{beta} partially controls 17-E2-mediated benefits on systemic metabolic regulation in female, but not male, mice, and that 17-E2 likely signals through ER{beta} in HSCs to attenuate pro-fibrotic mechanisms.

physiology↗

bioRxiv2022

17α-estradiol, a lifespan-extending compound, attenuates liver fibrosis by modulating collagen turnover rates in male mice

BackgroundEstrogen signaling is protective against chronic liver diseases, although men and a subset of women are contraindicated for chronic treatment with 17{beta}-estradiol (17{beta}-E2) or combination hormone replacement therapies. We sought to determine if 17-estradiol (17-E2), a naturally-occurring diastereomer of 17{beta}-E2, could attenuate liver fibrosis. MethodsWe evaluated the effects of 17-E2 treatment on collagen synthesis and degradation rates using tracer-based labeling approaches in male mice subjected to carbon tetrachloride (CCl4)-induced liver fibrosis. We also assessed the effects of 17-E2 on markers of hepatic stellate cell (HSC) activation, collagen crosslinking, collagen degradation, and liver macrophage content and polarity. FindingsWe found that 17-E2 significantly reduced collagen synthesis rates and increased collagen degradation rates, which was mirrored by declines in transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver. These improvements were associated with increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokines expression in the liver. InterpretationWe conclude that 17-E2 reduces fibrotic burden by suppressing HSC activation and enhancing collagen degradation mechanisms. Future studies will be needed to determine if 17-E2 acts directly in hepatocytes, HSCs, and/or immune cells to elicit these benefits. FundingThis work was supported by the US National Institutes of Health and US Department of Veterans Affairs. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe prevalence and severity of chronic liver diseases are greater in men than women and men are twice as likely to die from chronic liver diseases. However, the prevalence and severity of nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), and liver fibrosis becomes comparable between the sexes following menopause, particularly when hormone replacement therapies (HRT) are not initiated. These observations suggest that estrogen signaling is protective against liver disease onset and progression, which is supported by studies in rodents demonstrating that 17{beta}-estradiol (17{beta}-E2) ameliorates hepatic steatosis and fibrogenesis. However, chronic administration of 17{beta}-E2 or combination HRTs are unrealistic in men due to feminization and increased risk for stroke and prostate cancer, and a subset of the female population are also at an increased risk for breast cancer and cardiovascular events when on HRTs. Therefore, we have begun exploring the therapeutic potential of 17-estradiol (17-E2), a naturally-occurring, nonfeminizing, diastereomer of 17{beta}-E2, for the treatment of liver diseases. Added value of this studyIn this study, using tracer-based labeling approaches in male mice subjected to CCl4-induced liver fibrosis, we show that 17-E2 reduces liver fibrosis by attenuating collagen synthesis and enhancing collagen degradation mechanisms. Both transforming growth factor {beta}1 (TGF-{beta}1) and lysyl oxidase-like 2 (LOXL2) protein content in liver were reduced by 17-E2. We also found that 17-E2 increased matrix metalloproteinase 2 (MMP2) activity and suppressed stearoyl-coenzyme A desaturase 1 (SCD1) protein levels, the latter of which has been linked to the resolution of liver fibrosis. We also found that 17-E2 increased liver fetuin-A protein, a strong inhibitor of TGF-{beta}1 signaling, and reduced pro-inflammatory macrophage activation and cytokine expression in the liver. Implications of all the available evidenceThis study supports the idea that estrogens are protective against chronic liver diseases and that 17-E2 may have therapeutic utility for the treatment of liver fibrosis.

physiology↗

bioRxiv2022

Senolytic Treatment Reduces Cell Senescence and Necroptosis in Sod1 Knockout Mice that is Associated with Reduced Inflammation and Hepatocellular Carcinoma

The goal of this study was to test the role cellular senescence plays in the increase in inflammation, chronic liver disease, and hepatocellular carcinoma, which are seen in mice null for Cu/Zn-Superoxide dismutase (Sod1KO). To inhibit senescence, six-month-old wildtype (WT) and Sod1KO mice were given the senolytics, dasatinib and quercetin (D+Q) for seven months. D+Q treatment reduced the expression of p16 in the livers of Sod1KO mice to WT levels as well as the expression of several SASP (senescence associated secretory phenotype) factors (IL-6, IL-1{beta}, CXCL-1, and GDF-15). D+Q treatment also reduced markers of inflammation in livers of the Sod1KO mice, e.g., cytokines, chemokines, macropthage levels, and Kupffer cell clusters. D+Q treatment had no effect on various markers of liver fibrosis in the Sod1KO mice but reduced the expression of genes involved in liver cancer (Myc, Tgfbr2, Socs3, and Cdkn2a) as well as dramatically reducing the incidence of hepatocellular carcinoma. Surprisingly, D+Q also reduced markers of necroptosis (phosphorylated and oligomerized MLKL) in the Sod1KO mice to WT levels. We also found that inhibiting necroptosis in the Sod1KO mice with necrostatin-1s reduced the markers of cellular senescence (p16, p21, and p53). The data from our study suggest that an interaction occurs between cellular senescence and necroptosis in the liver of Sod1KO mice. We propose that these two cell fates interact through a positive feedback loop resulting in a cycle amplifying both cellular senescence and necroptosis leading to inflammaging and age-associated pathology in the Sod1KO mice.

biochemistry↗

bioRxiv2022

Pharmacological Interrogation of the C. elegans Pharyngeal Cuticle Reveals Small Molecule Amyloid Disruptors

Amyloids are associated with over 50 human diseases and have inspired significant effort to identify small molecule remedies. Here, we present a novel in vivo platform that efficiently yields small molecule disruptors of amyloid formation. We previously identified small molecules that kill the nematode C. elegans by forming membrane-piercing crystals in the pharynx cuticle, which is rich in amyloid-like material. We show here that many of these molecules are known amyloid-binders whose crystal-formation in the pharynx can be blocked by amyloid-binding dyes. Furthermore, we found that amyloid fibrils can seed small molecule crystal formation in vitro. These observations suggest that small molecule crystals are seeded by the cuticles amyloid-like material. We asked whether this phenomenon could be exploited to identify additional molecules that interfere with the ability of amyloids to seed higher-order structures. We screened 2560 compounds and identified 85 crystal suppressors, which we found to be 10-fold enriched in known amyloid disruptors relative to a random set. Of the uncharacterized suppressors, we found 25% to inhibit Ab42 fibril nucleation and/or extension in vitro, which is a hit rate that far exceeds other screening methodologies. Hence, screens for suppressors of crystal formation can efficiently reveal small molecules with amyloid-disrupting potential.

pharmacology and toxicology↗

bioRxiv2022

A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins

Roughly 4.5 million species of ecdysozoan animals repeatedly shed their old cuticle and construct a new one underneath to accommodate growth. How cuticles are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. 48% of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families that are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs that are introduced for the first time here. We find that all four families have sequence properties known to drive phase separation and show in vitro phase separation for one of these proteins. This systematic analysis reveals the massive contribution that IDPs make to the cuticle and highlights how reversibly phase-separating materials may facilitate cuticle disassembly and reassembly during the molt.

systems biology↗

bioRxiv2021

A comprehensive computational investigation into the conserved virulent proteins of Shigella sp unveils potential siRNA candidates as a new therapeutic strategy against shigellosis

Shigella sp account for the second-leading cause of deaths due to diarrheal diseases among children of less than 5 years of age. Emergence of multi-drug resistant Shigella isolates and the lack of availability of Shigella vaccines have made the efforts in the development of new therapeutic strategies against shigellosis very pertinent. In our study we have analyzed a total of 241 conserved sequences from a 15 different conserved virulence genes of Shigella sp and through extensive rational validation using a plethora of computational algorithms; we primarily obtained fifty eight small-interfering RNA (siRNA) candidates. Further extensive computational validation showed only three siRNA candidates that were found to exhibit substantial functional efficacy, be non-immunogenic and have a thermodynamically stable and sterically feasible and thereby acceptable tertiary structure. These siRNA candidates are intended to suppress the expression of the virulence genes, namely: IpgD (siRNA 9) and OspB (siRNA 15 and siRNA 17) and thus act as a prospective tool in the RNA interference (RNAi) pathway. However, the findings of our study require further wet lab validation and optimization for regular therapeutic use in the treatment of shigellosis.

bioinformatics↗

bioRxiv2020

A small molecule screen identified N-Acetyl-L-cysteine for promoting ex vivo growth of single circulating tumor cells

Circulating tumor cells (CTCs) can be isolated via a minimally invasive blood draw and are considered a "liquid biopsy" of their originating solid tumors. CTCs contain a small subset of metastatic precursors that can form metastases in secondary organs, and provide a resource to identify mechanisms underlying metastasis-initiating properties. Despite technological advancements that allow for highly sensitive approaches of detection and isolation, CTCs are very rare and often present as single cells, posing an extreme challenge for ex vivo expansion after isolation. Here, using previously established patient-derived CTC lines, we performed a small molecule drug screening to identify compounds that can improve ex vivo culture efficiency for single CTCs. We found that N-acetylcysteine (NAC) and other antioxidants can promote ex vivo expansion of single CTCs, by reducing oxidative and other stress particularly at the initial stage of single cell expansion. RNA-seq analysis of growing clones and non-growing clones confirmed the effect by NAC, but also indicate that NAC-induced decrease in oxidative stress is insufficient for promoting proliferation of a subset of cells with heterogeneous quiescent and senescent features. Despite the challenge in expanding all CTCs, NAC treatment lead to establishment of single CTC clones that have similar tumorigenic features, which will facilitate future functional analyses.

cancer biology↗

bioRxiv2019

MMP2 As An Independent Prognostic Stratifier In Oral Cavity Cancers

BackgroundAround 25% of oral cavity squamous cell carcinoma (OCSCC) are not controlled by standard of care. Identifying those patients could offer them possibilities for intensified and personalized regimen. However, there is currently no validated biomarker for OCSCC patient selection in a pre-treatment setting.\n\nPatients and methodsOur objectives were to determine a robust and independent predictive biomarker for disease related death in OCSCC treated with standard of care. Tumor and juxtatumor secretome were analyzed in a prospective discovery cohort of 37 OCSCC treated by primary surgery. Independent biomarker validation was performed by RTqPCR in a retrospective cohort of 145 patients with similar clinical features. An 18-gene signature (18G) predictive of the response to PD-1 blockade was evaluated in the same cohort..\n\nResultsAmong 29 deregulated molecules in a secretome analysis, we identified soluble MMP2 as a prognostic biomarker. In our validation cohort (n=145), high levels of MMP2 and CD276, and low levels of CXCL10 and STAT1 mRNA were associated with poor prognosis in univariate analysis (Kaplan-Meier). MMP2 (p = 0.001) and extra-nodal extension (ENE) (p = 0.006) were independent biomarkers of disease-specific survival (DSS) in multivariate analysis, and defined prognostic groups with 5-year DSS ranging from 36% (MMP2highENE+) to 88% (MMP2lowENE-). The expression of 18G was similar in the different prognostic groups, suggesting comparable responsiveness to anti-PD-1.\n\nConclusionHigh levels of MMP2 was an independent and validated prognostic biomarker, which may be used to select poor prognosis patients for intensified neoadjuvant or adjuvant regimens.

cancer biology↗

bioRxiv2019

PDL1 AND ICOSL DISCRIMINATE HUMAN SECRETORY AND HELPER DENDRITIC CELLS

Dendritic cells (DC) are described as immature at the steady state, with a high antigen capture capacity, turning into a mature state with a strong T cell stimulatory capacity upon activation. Using 16 different stimuli in vitro (130 observations), we describe two states of human activated dendritic cells. PDL1highICOSLlow \"secretory DC\" produced large amounts of inflammatory cytokines and chemokines but induced very low levels of T helper (Th) cytokines following DC-T co-culture; conversely PDL1lowICOSLhigh \"helper DC\" produced low levels of secreted factors but induced high levels of Th cytokines characteristic of a broad range of Th subsets. Secretory DC were phenotypically identified in T cell inflamed primary head and neck squamous cell carcinoma. RNAseq analysis showed that they expressed a typical secretory DC signature, including CD40, PVR, IL1B, TNF, and CCL19. This novel and universal functional dichotomy of human DC opens broad perspectives for the characterization of inflammatory diseases, and for immunotherapy.

immunology↗

bioRxiv2019

The Marginal Cells of the Caenorhabditis elegans Pharynx Scavenge Cholesterol and Other Hydrophobic Small Molecules

The nematode worm Caenorhabditis elegans is a bacterivore filter feeder. Through the contraction of the worms pharynx, a bacterial suspension is sucked into the pharynxs lumen. Excess liquid is then shunted out of the buccal cavity through ancillary channels that are made from specialized pharyngeal cells called marginal cells. Through the characterization of our library of worm-bioactive small molecules (a.k.a. wactives), we found that more than one third of wactives visibly accumulate inside of the marginal cells as crystals or globular spheres. Wactives that visibly accumulate are typically more hydrophobic than those that do not. To understand why wactives accumulate specifically in marginal cells, we performed a forward genetic screen for mutants that resist the lethality associated with one crystallizing wactive. We identified a presumptive sphingomyelin-synthesis pathway that is necessary for crystal and sphere accumulation. Sphingomyelin is a phospholipid that is enriched in the outer leaflet of the plasma membranes of most metazoans. We find that the predicted terminal enzyme of this pathway, sphingomyelin synthase 5 (SMS-5), is expressed in the pharynx, contributes to sphingomyelin abundance, and that its expression in marginal cells is sufficient for wactive accumulation. We also find that the expression of SMS-5 in the marginal cells is necessary for the proper absorption of exogenous cholesterol, without which C. elegans cannot develop. We conclude that the sphingomyelin-rich plasma membrane of the marginal cells acts as a sink to scavenge important hydrophobic nutrients from the filtered liquid that might otherwise be shunted back into the environment. One sentence summaryThe anterior pharynx of C. elegans is a Sink for Hydrophobic Small Molecules

developmental biology↗

bioRxiv2017

Imaging-Genomics Study Of Head-Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes And Genomic Mechanisms Via Integration Of TCGA And TCIA

PurposeRecent data suggest that imaging radiomics features for a tumor could predict important genomic biomarkers. Understanding the relationship between radiomic and genomic features is important for basic cancer research and future patient care. For Head and Neck Squamous Cell Carcinoma (HNSCC), we perform a comprehensive study to discover the imaging-genomics associations and explore the potential of predicting tumor genomic alternations using radiomic features.\n\nMethodsOur retrospective study integrates whole-genome multi-omics data from The Cancer Genome Atlas (TCGA) with matched computed tomography imaging data from The Cancer Imaging Archive (TCIA) for the same set of 126 HNSCC patients. Linear regression analysis and gene set enrichment analysis are used to identify statistically significant associations between radiomic imaging features and genomic features. Random forest classifier is used to predict two key HNSCC molecular biomarkers, the status of human papilloma virus (HPV) and disruptive TP53 mutation, based on radiomic features.\n\nResultsWide-spread and statistically significant associations are discovered between genomic features (including miRNA expressions, protein expressions, somatic mutations, and transcriptional activities, copy number variations, and promoter region DNA methylation changes of pathways) and radiomic features characterizing the size, shape, and texture of tumor. Prediction of HPV and TP53 mutation status using radiomic features achieves an area under the receiver operating characteristics curve (AUC) of 0.71 and 0.641, respectively.\n\nConclusionOur analysis suggests that radiomic features are associated with genomic characteristics in HNSCC and provides justification for continued development of radiomics as biomarkers for relevant genomic alterations in HNSCC.

cancer biology↗