Biology subjects

Jiang, X.

Publications and source records attributed to Jiang, X..

At least 307 records · Page 17Linked to original sources

bioRxiv2021

Open Imputation Server provides secure Imputation services with provable genomic privacy

SummaryAs DNA sequencing data is available for personal use, genomic privacy is becoming a major challenge. Nevertheless, high-throughput genomic data analysis outsourcing is performed using pipelines that tend to overlook these challenges. ResultsWe present a client-server-based outsourcing framework for genotype imputation, an important step in genomic data analyses. Genotype data is encrypted by the client and encrypted data are used by the server that never observes the data in plain. Cloud-based framework can benefit from virtually unlimited computational resources while providing provable confidentiality. We demonstrate servers utility from several aspects using genotype dataset from the 1000 Genomes datasets. First, we benchmark the accuracy of common variant imputation in comparison to BEAGLE, a state-of-the-art imputation method. We also provide the detailed time requirements of the server to showcase scaling of time usage in different steps of imputation. We also present a simple correlation metric that can be used to estimate imputation accuracy using only the reference panels. This is important for filtering the variants in downstream analyses. As a further demonstration and a different use case, we performed a simulated genomewide association study (GWAS) using imputed and known genotypes and highlight potential utility of the server for association studies. Overall, our study present multiple lines of evidence for usability of secure imputation service. AvailabilityServer is publicly available at https://www.secureomics.org/OpenImpute. Users can anonymously test and use imputation server without registration. ContactArif.O.Harmanci@uth.tmc.edu

bioinformatics↗

bioRxiv2021

SVAT: Secure Outsourcing of Variant Annotation and Genotype Aggregation

BackgroundSequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight for genetic determinants of diseases. Protecting the genetic privacy of participants is challenging as only a few rare variants can easily re-identify an individual among millions. In certain cases, there are policy barriers against sharing genetic data from indigenous populations and stigmatizing conditions. ResultsWe present SVAT, a method for secure outsourcing of variant annotation and aggregation, which are two basic steps in variant interpretation and detection of causal variants. SVAT uses homomorphic encryption to encrypt the data at the client-side. The data always stays encrypted while it is stored, in-transit, and most importantly while it is analyzed. SVAT makes use of a vectorized data representation to convert annotation and aggregation into efficient vectorized operations in a single framework. Also, SVAT utilizes a secure re-encryption approach so that multiple disparate genotype datasets can be combined for federated aggregation and secure computation of allele frequencies on the aggregated dataset. ConclusionsOverall, SVAT provides a secure, flexible, and practical framework for privacy-aware outsourcing of annotation, filtering, and aggregation of genetic variants. SVAT is publicly available for download from https://github.com/harmancilab/SVAT

bioinformatics↗

bioRxiv2021

Evaluation of Vicinity-based Hidden Markov Models for Genotype Imputation

The decreasing cost of DNA sequencing has led to a great increase in our knowledge about genetic variation. While population-scale projects bring important insight into genotype-phenotype relationships, the cost of performing whole-genome sequencing on large samples is still prohibitive. In-silico genotype imputation coupled with genotyping-by-arrays is a cost-effective and accurate alternative for genotyping of common and uncommon variants. Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium patterns. Most accurate imputation methods are based on the Li-Stephens hidden Markov model, HMM, that treats the sequence of each chromosome as a mosaic of the haplotypes from the reference panel. Here we assess the accuracy of local-HMMs, where each untyped variant is imputed using the typed variants in a small window around itself (as small as 1 centimorgan). Locality-based imputation is used recently by machine learning-based genotype imputation approaches. We assess how the parameters of the local-HMMs impact the imputation accuracy in a comprehensive set of benchmarks and show that local-HMMs can accurately impute common and uncommon variants and can be relaxed to impute rare variants as well. The source code for the local HMM implementations is publicly available at https://github.com/harmancilab/LoHaMMer.

bioinformatics↗

bioRxiv2021

The secretome of M1 and M2 microglia differently regulate proliferation, differentiation and survival of adult neural stem/progenitor cell

Microglia has been reported to be able to regulate the proliferation, differentiation and survival of adult Neural stem/progenitor cells (NSPCs) by modulating the microenvironment, which results in different consequences of adult neurogenesis. However, whether the microglial activation is beneficial or harmful to NSPCs is still controversial because of the complexity and variability of microglial activation phenotypes. In this study, we detected the expression levels of M1 marker and M2 marker in IFN-{gamma}- and IL-4-induced microglia at different time, respectively. The phenotypic markers of M1 and M2 microglia were stable for 24 h after removal of IFN-{gamma} and IL-4 intervention, but exhibited different change patterns during the next 24 h. Then, the adult NSPCs were treated by the conditioned medium from IFN-{gamma}- and IL-4-activated microglia. The conditioned medium from IFN-{gamma}-activated microglia promoted apoptosis and astroglial differentiation of NSPCs, while suppressed proliferation and neuronal differentiation of NSPCs. However, the conditioned medium from IL-4-activated microglia exhibited opposite effects on these physiological processes. In addition, the direct treatment of IFN-{gamma} or IL-4 alone did not significantly affect the proliferation, differentiation and survival of NSPCs. These results suggest that the secretome of pro-inflammatory (M1) and anti-inflammatory (M2) microglia differently regulated the proliferation, differentiation and survival of adult NSPCs. These findings will help further study the biological mechanism of microglia regulating neurogenesis, and provide a therapeutic strategy for neurological diseases by regulating microglial phenotypes to affect neurogenesis.

neuroscience↗

bioRxiv2021

A high throughput bispecific antibody discovery pipeline

Bispecific antibodies (BsAbs) represent an emerging class of immunotherapy but inefficiency in the current BsAb discovery paradigm has limited their broad clinical availability. Here we report a high throughput, agnostic, single-cell-based BsAb functional screening pipeline, comprising molecular and cell engineering for efficient generation of BsAb library cells, followed by functional interrogation at the single-cell level to identify and sort positive clones and downstream sequence identification with single-cell PCR and sequencing and functionality characterization. Using a CD19xCD3 bispecific T cell engager (BiTE) as a model system, we demonstrate that our single cell platform possesses a high throughput screening efficiency of up to one and half million variant library cells per run and can isolate rare functional clones at low abundance of 0.008%. Using a complex CD19xCD3 BiTE-expressing cell library with approximately 22,300 unique variants comprising combinatorially varied scFvs, connecting linkers and VL/VH orientations, we have identified 98 unique clones including extremely rare ones ([~] 0.001% abundance). We also discovered BiTEs that exhibit novel properties contradictory to conventional wisdom, including harboring rigid scFv connecting peptide linkers yet with in vitro cytotoxicity comparable to that of clinically approved Blinatumomab. Through sequencing analyses on sorted BiTE clones, we discovered multiple design variable preferences for functionality including the CD19VL-VH- CD3VH-VL and CD19VH-VL-CD3VH-VL arrangements being the most favored orientation. Sequence analysis further interrogated the sequence composition of the CDRH3 domain in scFvs and identified amino acid residues conserved for function. We expect our single cell platform to not only significantly increase the development speed of high quality of new BsAb therapeutics for cancer and other disorders, but also enable identifying generalizable design principles for new BsAbs and other immunotherapeutics based on an in-depth understanding of the inter-relationships between sequence, structure, and function.

bioengineering↗

bioRxiv2021

Common and distinct neurofunctional representations of core and social disgust in the brain: An ALE meta-analysis and MACM characterization

Disgust represents a multifaceted defensive-avoidance response. On the behavioral level, the response includes withdrawal and a disgust-specific facial expression. While both serve the avoidance of pathogens, the latter additionally transmits social-communicative information. Given that common and distinct brain representation of the primary defensive-avoidance response (core disgust) and encoding of the social-communicative signal (social disgust) remain debated, we employed neuroimaging meta-analyses to (1) determine brain systems generally engaged in disgust processing, and (2) segregate common and distinct brain systems for core and social disgust. Disgust processing, in general, engaged a bilateral network encompassing the insula, amygdala, occipital and prefrontal regions. Core disgust evoked stronger reactivity in left-lateralized threat detection and defensive response network including amygdala, occipital and frontal regions while social disgust engaged a right-lateralized superior temporal-frontal network engaged in social cognition. Anterior insula, inferior frontal and fusiform regions were commonly engaged during core and social disgust, suggesting a common neural basis. We demonstrate a common and separable neural basis of primary disgust responses and encoding of associated social-communicative signals.

neuroscience↗

bioRxiv2021

Human spindle variability

In humans, sleep spindles are 10-16 Hz oscillations lasting approximately 0.5-2 s. Spindles, along with cortical slow oscillations, facilitate memory consolidation by enabling synaptic plasticity. Early recordings of spindles at the scalp found anterior channels had overall slower frequency than central-posterior channels. This robust, topographical finding led to dichotomizing spindles as slow versus fast, modelled as two distinct spindle generators in frontal versus posterior cortex. Using a large dataset of intracranial sEEG recordings (n=20, 365 bipolar recordings), we show that the difference in spindle frequency between frontal and parietal channels is comparable to the variability in spindle frequency within the course of individual spindles, across different spindles recorded by a given site, and across sites within a given region. Thus, fast and slow spindles only capture average differences that obscure a much larger underlying overlap in frequency. Furthermore, differences in mean frequency are only one of several ways that spindles differ. For example, compared to parietal, frontal spindles are smaller, tend to occur after parietal when both are engaged, and show a larger decrease in frequency within-spindles. However, frontal and parietal spindles are similar in being longer, less variable, and more widespread than occipital, temporal, and Rolandic spindles. These characteristics are accentuated in spindles which are highly phase-locked to posterior hippocampal spindles. We propose that rather than a strict parietal-fast/frontal-slow dichotomy, spindles differ continuously and quasi-independently in multiple dimensions, with variability due about equally to within-spindle, within-region and between-region factors. Significance StatementSleep spindles are 10-16 Hz neural oscillations generated by cortico-thalamic circuits that promote memory consolidation. Spindles are often dichotomized into slow-anterior and fast-posterior categories for cognitive and clinical studies. Here, we show that the anterior-posterior difference in spindle frequency is comparable to that observed between different cycles of individual spindles, between spindles from a given site, or from different sites within a region. Further, we show that spindles vary on other dimensions such as duration, amplitude, spread, primacy and consistency, and that these multiple dimensions vary continuously and largely independently across cortical regions. These findings suggest that multiple continuous variables rather than a strict frequency dichotomy may be more useful biomarkers for memory consolidation or psychiatric disorders.

neuroscience↗

bioRxiv2021

Patient-Derived Three-Dimensional Cortical Neurospheres to Model Parkinson's Disease

There are currently no preventive or disease-modifying therapies for Parkinsons Disease (PD). Failures in clinical trials necessitate a re-evaluation of existing pre-clinical models in order to adopt systems that better recapitulate underlying disease mechanisms and better predict clinical outcomes. In recent years, models utilizing patient-derived induced pluripotent stem cells (iPSCs) have emerged as attractive models to recapitulate disease-relevant neuropathology in vitro without exogenous overexpression of disease-related pathologic proteins. Here, we utilized iPSCs derived from patients with early-onset PD and dementia phenotypes that harbored either a point mutation (A53T) or multiplication at the -synuclein/SNCA gene locus. We generated a three-dimensional (3D) cortical neurosphere culture model to better mimic the tissue microenvironment of the brain. We extensively characterized the differentiation process using quantitative PCR, Western immunoblotting and immunofluorescence staining. Differentiation and aging of the neurospheres revealed alterations in fatty acid profiles and elevated total and pathogenic phospho--synuclein levels in both A53T and the triplication lines compared to their isogenic control lines. Furthermore, treatment of the neurospheres with a small molecule inhibitor of stearoyl CoA desaturase (SCD) attenuated the protein accumulation and aberrant fatty acid profile phenotypes. Our findings suggest that the 3D cortical neurosphere model is a useful tool to interrogate targets for PD and amenable to test small molecule therapeutics.

neuroscience↗

bioRxiv2021

miR-206 inhibits estrogen-induced proliferation and invasion of ER-α36 positive gastric cancer cells

ObjectiveTo explore the biological role of miR-206 in inhibiting the proliferation and invasion of estrogen-induced ER-36 positive gastric cancer cells and its related mechanisms. MethodsMTT and tranwell assays were used to detect the proliferation and invasion of BGC-823 cells under different concentrations and time of ER stimulation. RT-PCR was used to detect the effect of ER stimulation on the content of miR-206 in gastric cancer cells. miR-206 mimics were transfected into BGC-823 cells to detect cell proliferation and invasion; luciferase reporter assay was used to determine whether miR-206 targets the 3-untranslated region of the CDK14-encoding gene (3 -UTR). ResultsWe confirmed that estrogen promoted the proliferation and invasion of BGC-823 cells; As the concentration of estrogen increases, the level of miR206 in the cell gradually rises.Overexpression of miR-206 significantly decreased the estrogen-induced BGC-823 cells. Proliferative and invasive ability; miR-206 inhibits the expression of CDK14 by directly binding to the 3-UTR of CDK14 mRNA, thereby inhibiting the proliferation and invasion of gastric cancer cells. ConclusionsOur results suggest that miR-206 inhibits estrogen-induced proliferation and invasion of ER-36-positive gastric cancer cells by inhibiting CDK14 and may be a promising therapeutic option for anticancer therapy.

cancer biology↗

bioRxiv2021

Mining bacterial NGS data vastly expands the complete genomes of temperate phages

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis1. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to the lysogenicity of these phages, which curb the identification and characterization of temperate phages. Existing in silico tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes2-5. In this study, by a novel computational method mining both the integrated active prophages and their spontaneously induced forms (temperate phages), we obtained 192,326 complete temperate phage genomes from bacterial next-generation sequencing (NGS) data, hence expanded the existing number of complete temperate phage genomes by more than 100-fold. The reliability of our method was validated by wet-lab experiments. The experiments demonstrated that our method can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites (attP and attB sites), outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the evolution of microbes by 1) cross-infecting different bacterial host species; 2) transferring antibiotic resistance and virulence genes; and 3) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensive complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.

bioinformatics↗

bioRxiv2021

Novel low-avidity glypican-3 specific CARTs resist exhaustion and mediate durable antitumor effects against hepatocellular carcinoma

Chimeric antigen receptor engineered T cells (CARTs) are being developed to treat solid tumors including hepatocellular carcinoma (HCC). However, thus far, CARTs have not been as effective against solid tumors as compared to blood cancers. A main reason is that, once infiltrating into a solid tumor mass, CARTs are surrounded and chronically stimulated by persistent target antigens, which may drive them to exhaustion. We hypothesize that, due to weak engagement, low-avidity CARTs will resist the antigen-driven exhaustion and apoptosis and maintain effector functions in solid tumors, generating durable antitumor effects. To test this idea, we developed a novel human glypican-3 (hGPC3) specific antibody (8F8) that binds an epitope close to that of GC33 (the frequently used high-affinity antibody), but with ~17 folds lower affinity. In vitro, the low-avidity 8F8 CART killed tumor cells and produced effector cytokines to the same extent as high-avidity GC33 CART. Remarkably, however, 8F8 CART expanded and persisted to a greater extent than GC33 CART in vivo, resulting in durable responses against HCC xenografts. Compared to GC33 CARTs, there were significantly more (5 times) 8F8-BBz CART detected in the tumor mass. Importantly, the tumor infiltrating 8F8 CARTs were less apoptotic and more resistant to exhaustion, revealed by their enhanced and durable effector functions overtime. We predict that this novel low-avidity 8F8-BBz CART has a greater potential than mainstream high-avidity CARTs in effectively treating patients with HCC or other hGPC3+ solid tumors.

immunology↗

bioRxiv2021

Reflective mirror-based line-scan adaptive optics OCT

Line-scan OCT, incorporated with adaptive optics (AO), offers high resolution, speed and sensitivity for imaging retinal structure and function in vivo. Here, we introduce its implementation with reflective mirror-based afocal telescopes, optimized for imaging light-induced retinal activity (optoretinography) and weak retinal reflections at the cellular scale. A non-planar optical design was followed based on previous recommendations with key differences specific to a line-scan geometry. The three beam paths fundamental to an OCT system - illumination/sample, detection, and reference - were modeled in Zemax optical design software to yield theoretically diffraction-limited performance over a 2.2 deg. field-of-view and 1.5 D vergence range at the eyes pupil. The performance for imaging retinal structure was exemplified by cellular-scale visualization of retinal ganglion cells, macrophages, foveal cones, and rods in human observers. The performance for functional imaging was exemplified by resolving the light-evoked optical changes in foveal cone photoreceptors where the spatial resolution was sufficient for cone spectral classification at an eccentricity 0.3 deg. from the foveal center. This enabled the first in vivo demonstration of reduced S-cone (short-wavelength cone) density in the human foveola, thus far observed only in ex vivo histological preparations. Together, the feasibility for high resolution imaging of retinal structure and function demonstrated here holds significant potential for basic science and translational applications.

bioengineering↗

bioRxiv2021

Single-cell anatomical analysis of human hippocampus and entorhinal cortex uncovers early-stage molecular pathology in Alzheimer's disease

The human hippocampal formation plays a central role in Alzheimers disease (AD) progression, cognitive traits, and the onset of dementia; yet its molecular states in AD remain uncharacterized. Here, we report a comprehensive single-cell transcriptomic dissection of the human hippocampus and entorhinal cortex across 489,558 cells from 65 individuals with varying stages of AD pathology. We transcriptionally characterize major brain cell types and neuronal classes, including 17 glutamatergic and 8 GABAergic neuron subpopulations. Combining evidence from human and mouse tissue-microdissection, neuronal cell isolation and spatial transcriptomics, we show that single-cell expression patterns capture fine-resolution neuronal anatomical topography. By stratifying subjects into early and late pathology groups, we uncover stage-dependent and cell-type specific transcriptional modules altered during AD progression. These include early-stage cell-type specific dysregulation of cellular and cholesterol metabolism, late-stage neuron-glia alterations in neurotransmission, and late-stage signatures of cellular stress, apoptosis, and DNA damage broadly shared across cell types. Late-stage signatures show signs of convergence in hippocampal and cortical cells, while early changes diverge; highlighting the relevance of characterizing molecular pathology across brain regions and AD progression. Finally, we characterize neuron subregion-specific responses to AD pathology and show that CA1 pyramidal neurons are the most transcriptionally altered while CA3 and dentate gyrus granule neurons the least. Our study provides a valuable resource to extend cell type-specific studies of AD to clinically relevant brain regions affected early by pathology in disease progression.

neuroscience↗

bioRxiv2021

Psychophysiological Evidence for Fear Extinction Learning via Mental Imagery

Imagery-based extinction procedures have long been used in the treatments of fear-related conditions. The assumption is that imagery can substitute for the perceptual stimuli in the extinction process. Yet, experimental validations of this assumption have been limited in number and some have relied exclusively on measures of autonomic reactivity without consideration of conscious feelings of fear. The current investigation sought to assess whether imagery-based exposure could lead to extinction of conditioned fear to the corresponding perceptual stimulus. Conditioned fear responses were measured by both a physiological (i.e., skin conductance response/SCR) and a subjective (i.e., self-reported fear) measure. Participants (N = 56) first underwent perceptual differential fear conditioning, then imagery extinction, then perceptual extinction. SCR evidence was found for successful fear conditioning, generalization of fear from viewing to imagery, and most importantly, the absence of differential fear after imagery extinction upon re-exposure to the conditioned perceptual stimulus. Self-reported fear confirmed the acquisition and generalization of fear and provided evidence of a significant reduction in differential fear conditioning across extinction. Consistent with clinical evidence of the efficacy of imagery extinction and the existing limited experimental literature, the current study offers support for fear extinction to perceptual stimuli via imagery exposure.

neuroscience↗

bioRxiv2021

A CRISPR toolbox for generating intersectional genetic mice for functional, molecular, and anatomical circuit mapping

BackgroundA full understanding of circuits and cellular mechanisms governing health and disease requires the dissection and multi-faceted study of discrete cell subtypes in developing and adult animal models. Recombinase-driven expression of transgenic response alleles represents a significant and powerful approach to delineate cell populations for functional, molecular, and anatomical study. In addition to single recombinase systems, the expression of two recombinases in distinct, but partially overlapping, populations allow for more defined target expression. Although the application of this method is becoming increasingly popular, the expense and difficulty associated with production of customized intersectional mouse lines have limited widespread application to more common allele manipulations that are often commercially produced at great expense. ResultsWe present a simplified CRISPR toolkit for rapid, inexpensive, and facile intersectional allele production. Briefly, we produced 7 intersectional mouse lines using a dual recombinase system, one mouse line with a single recombinase system, and three embryonic stem (ES) cell lines that are designed to study how functional, molecular, and anatomical features relate to each other in building circuits that underlie physiology and behavior. As a proof-of-principle, we applied three of these lines to different neuronal populations for anatomical mapping and functional in vivo investigation of respiratory control. We also generated a mouse line with a single recombinase-responsive allele that controls the expression of the calcium sensor Twitch-2B. This mouse line was applied globally to study the effects of follicle stimulating hormone (FSH) and luteinizing hormone (LH) on calcium release in the ovarian follicle. ConclusionsLines presented here are representative examples of outcomes possible with the successful application of our genetic toolkit for the facile development of diverse, modifiable animal models. This toolkit will allow labs to create single or dual recombinase effector lines easily for any cell population or subpopulation of interest when paired with the appropriate Cre and FLP recombinase mouse lines or viral vectors. We have made our tools and derivative intersectional mouse and ES cell lines openly available for non-commercial use through publicly curated repositories for plasmid DNA, ES cells, and transgenic mouse lines.

genetics↗

bioRxiv2021

Comprehensive Analysis of Spatial Architecture in Primary Liver Cancer

Heterogeneity is the major challenge for cancer prevention and therapy. Here, we firstly constructed high-resolution spatial transcriptomes of primary liver cancers (PLCs) containing 84,823 spots within 21 tissues from 7 patients. The sequential comparison of spatial tumor microenvironment (TME) characteristics from non-tumor to leading-edge to tumor regions revealed that the tumor capsule potentially affects intratumor spatial cluster continuity, transcriptome diversity and immune cell infiltration. Locally, we found that the bidirectional ligand-receptor interactions at the 100 m wide cluster-cluster boundary contribute to maintaining intratumor architecture. Our study provides novel insights for diverse tumor ecosystem of PLCs and has potential benefits for cancer intervention.

cancer biology↗

bioRxiv2021

CmP signaling network unveils novel biomarkers for triple negative breast cancer in African American women

Breast cancer is the most commonly diagnosed cancer worldwide and remains the second leading cause of cancer death. While breast cancer mortality has steadily declined over the past decades through medical advances, an alarming disparity in breast cancer mortality has emerged between African American women (AAW) and Caucasian American women (CAW); and new evidence suggests more aggressive behavior of triple-negative breast cancer (TNBC) in AAW may contribute to racial differences in tumor biology and mortality. Progesterone (PRG) is capable of exerting its cellular effects through either its classic, non-classic or combined responses through binding to either classic nuclear PRG receptors (nPRs) or non-classic membrane PRG receptors (mPRs), warranting both pathways an equally important status in PRG-mediated signaling. In our previous report, we demonstrated that the CCM signaling complex (CSC) consisting of CCM1, CCM2, and CCM3 proteins can couple both nPRs and mPRs signaling cascades to form a CSC-mPRs-PRG-nPRs (CmPn) signaling network in nPR positive(+) breast cancer cells. In this report, we furthered our research by establishing the CSC-mPRs-PRG (CmP) signaling network in nPR(-) breast cancer cells, demonstrating that a common core mechanism exists, regardless of nPR(+/-) cell type. This is the first report stating that inducible expression patterns exist between CCMs and major mPRs in TNBC cells. Furthermore, we firstly show mPRs in TNBC cells are localized in the nucleus and participate in nucleocytoplasmic shuttling in a coordinately synchronized fashion with CCM proteins under steroid actions, following the same cellular distribution as other well-defined steroid hormone receptors. Finally, for the first time, we deconvoluted the CmP signalosome by using multi-omics approaches, which helped us understand key factors within the CmP network, and identify 21 specific biomarkers with potential clinical applications associated with AAW-TNBC tumorigenesis. These novel biomarkers could have immediate clinical implications to dramatically improve health disparities among AAW-TNBCs.

cancer biology↗

bioRxiv2021

A novel SERPINE1-FOSB fusion gene in a case of pseudomyogenic hemangioendothelioma results in activation of intact FOSB and the PI3K-AKT-mTOR signaling pathway and responsiveness to sirolimus

Pseudomyogenic hemangioendothelioma (PHE) is an extremely rare disease that affects mainly the young and more men than women. PHE are multicentric, locally aggressive, have low metastatic potential, and affect multiple tissue planes. Genetic aberrations are frequently detected in PHE and may play important roles in the occurrence, development, and treatment of this disease. In this study, we report a case of PHE with a novel SERPINE1-FOSB fusion gene. The fusion introduced a strong promoter near the coding region of FOSB, resulting in overexpression of intact FOSB. Immunohistochemical analysis showed overexpression of pAKT and mTOR in tumor cells, suggesting activation of the PI3K-AKT-mTOR signaling pathway. The patient responded well to targeted therapy with sirolimus, an mTOR inhibitor. Our study correlated dysregulation of a specific signaling pathway and the effectiveness of a targeted therapy to a specific genetic aberration. This information may be useful for future investigations of targeted therapeutics and provide a potential predictive biomarker for therapeutic effectiveness in cases of PHE with this genetic aberration.

genetics↗