Xingyue He

Bio: Xingyue He is an academic researcher from Watson School of Biological Sciences. The author has contributed to research in topics: KRAS & Cancer research. The author has an hindex of 2, co-authored 2 publications receiving 2973 citations. Previous affiliations of Xingyue He include Stony Brook University.

A microRNA component of the p53 tumour suppressor network

Abstract: A global decrease in microRNA (miRNA) levels is often observed in human cancers, indicating that small RNAs may have an intrinsic function in tumour suppression. To identify miRNA components of tumour suppressor pathways, we compared miRNA expression profiles of wild-type and p53-deficient cells. Here we describe a family of miRNAs, miR-34a-c, whose expression reflected p53 status. Genes encoding miRNAs in the miR-34 family are direct transcriptional targets of p53, whose induction by DNA damage and oncogenic stress depends on p53 both in vitro and in vivo. Ectopic expression of miR-34 induces cell cycle arrest in both primary and tumour-derived cell lines, which is consistent with the observed ability of miR-34 to downregulate a programme of genes promoting cell cycle progression. The p53 network suppresses tumour formation through the coordinated activation of multiple transcriptional targets, and miR-34 may act in concert with other effectors to inhibit inappropriate cell proliferation.

Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation

Abstract: DNA methylation has important functions in stable, transcriptional gene silencing, immobilization of transposable elements and genome organization. In Arabidopsis, DNA methylation can be induced by double-stranded RNA through the RNA interference (RNAi) pathway, a response known as RNA-directed DNA methylation. This requires a specialized set of RNAi components, including ARGONAUTE4 (AGO4). Here we show that AGO4 binds to small RNAs including small interfering RNAs (siRNAs) originating from transposable and repetitive elements, and cleaves target RNA transcripts. Single mutations in the Asp-Asp-His catalytic motif of AGO4 do not affect siRNA-binding activity but abolish its catalytic potential. siRNA accumulation and non-CpG DNA methylation at some loci require the catalytic activity of AGO4, whereas others are less dependent on this activity. Our results are consistent with a model in which AGO4 can function at target loci through two distinct and separable mechanisms. First, AGO4 can recruit components that signal DNA methylation in a manner independent of its catalytic activity. Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects.

Electrical activities, excitability and multistability transitions of the hybrid neuronal model induced by electromagnetic induction and autapse

Abstract: Electromagnetic induction and autapse play important roles in regulating the electric activities, excitability, and bistable structure of neurons. The firing activities and global bifurcation patterns of a four-dimensional (4D) hybrid neuron model that combines the fast dynamic variables of the Wilson model and the slow feedback variables of the Hindmarsh–Rose (HR) model and magnetic flux are investigated based on the Matcont software and numerical calculation. The effect of electrical autapse on the dynamic evolution of the system is also discussed emphatically. Upon encountering electromagnetic induction, the hybrid neuron model exhibits complex global stability, Hopf bifurcation, and saddle-node bifurcation. Intriguingly, the system presents initial sensitivity and a bistable structure consisting of quiescent and period-1 spiking near the Hopf bifurcation point. It is worth noting that the feedback type of electrical autapse, including positive and negative feedback, has completely different effects on this bistable structure. Notably, the negative feedback autapse can expand and change the bistable region, so that the system generates a new bistable structure consisting of quiescent and periodic bursting states, and its bursting activities are also promoted. Moreover, extensive numerical results show that the system generally maintains a comb-shaped chaotic structure, abundant bifurcation patterns, and multistability. It should be noted that electrical autapse feedback types and time delays do not change the regular bifurcation structures but operate a complex regulatory mechanism for the coexistence of multiple attractors. These results will provide useful insights into the neuron’s dynamics under the atmosphere of electromagnetic induction and also electrical autapse.

244 AFNT-111, a safe and effective TCR-engineered T cell therapy targeting the oncogenic driver KRAS G12V mutation

Abstract: Background Mutations in the RAS family of genes are respon-sible for approximately 30% of all human cancers. Mutated RAS proteins are truncal oncogenic driver antigens essential for cancer development and progression making them optimal targets for cancer therapies by limiting tumor escape. The AFNT-111 cell therapy consists of autologous CD8 + and CD4 + T cells expressing a TCR specific for the highly preva-lent KRAS G12V mutation presented by HLA-A*11:01, one of the most common HLA alleles worldwide. AFNT-111 is also engineered to express the CD8 a / b coreceptor, enabling a coor-dinated CD4 + /CD8 + tumor response that aims to promote increased T cell activity and persistence while minimizing T cell exhaustion. G12V no reactivity to wildtype KRAS. Sev-eral naturally KRAS G12V cell lines, from colorectal, and pancreatic AFNT-111 T cell activation and proliferation, cytotoxicity towards In vitro killing AFNT-111 consistently repeated in

342 KRAS G12V T cell receptor-engineered T cells expressing the durability FAS-41BB switch receptor exhibit a potent, persistent, coordinated CD4/CD8 anti-tumor responsein vitroandin vivo

Abstract:

Background

Adoptive cell therapy with genetically modified T cells has shown promising efficacy in solid tumors but has been limited by immunosuppressive mechanisms that interfere with sustained activity including FAS ligand-induced apoptosis of tumor-infiltrating, FAS receptor-positive lymphocytes.¹ As previously reported, T Cell Receptor (TCR)-engineered T cells expressing a FAS-41BB switch receptor, consisting of FAS extracellular and 41BB intracellular domains, demonstrated improved anti-tumor efficacy.² KRAS is a frequently mutated oncogene in cancers³ and recent clinical evidence suggests that it is immunogenic and targetable via TCR-engineered T cells.⁴ Targeting a mutated oncogenic driver such as KRAS G12V offers many advantages, including tumor dependence driving homogenous expression and decreasing risk of therapeutic escape. We are now reporting an optimized construct that achieves high functional co-expression of the KRAS TCR, CD8ab, and FAS-41BB switch receptor in a single viral vector.

Methods

Human T cells isolated from healthy volunteers were lentivirally transduced with constructs encoding the KRAS TCR, CD8ab chains, and FAS-41BB. Preclinical studies included peptide titrations with the index peptide and ones in which one residue was individually substituted to all possible amino acids (XScan), co-cultures with tumors or B-LCL, and in vivo subcutaneous xenografts.

Results

Co-expression of CD8ab with the KRAS G12V-specific TCR allowed for efficient stimulation of CD4⁺ T cells, and further engineering with the FAS-41BB switch receptor increased sensitivity to low peptide concentrations. In tumor co-culture assays, the inclusion of FAS-41BB allowed for tumor control, even after re-challenge with fresh addition of tumor cells. In a repetitive T cell transfer/tumor exposure assay, continued proliferation and tumor control required both expression of FAS-41BB and inclusion of engineered CD4 and CD8 T cells, suggesting that CD8ab exogenous expression in CD4 T cells allowed for a coordinated T cell response able to resist exhaustion. Intravenous administration of engineered T cells prevented tumor outgrowth in vivo. Using the XScan assay, no off-target liabilities were identified upon co-incubation of A11-KRAS G12V/CD8ab/FAS-41BB switch receptor engineered T cells with all possible peptides in the human proteome matching the recognition motif, demonstrating the specificity of our TCR. No alloreactivity to the most prevalent HLA alleles was detected in B-LCL co-cultures.

Conclusions

Preclinical development of the KRAS G12V-specific TCR with co-expression of CD8ab and the durability FAS-41BB switch receptor supports the clinical development of this first-in-class product for solid tumor patients with high unmet medical needs.

References

Yamamoto TN, Lee P-H, Vodnala SK, Gurusamy D, Kishton RJ, Yu Z, Eidizadeh A, Eil R, Fioravanti J, Gattinoni L, Kochenderfer JN, Fry TJ, Aksoy BA, Hammerbacher J, Cruz AC, Siegel RM, Restifo NP, Klebanoff CA. T cells genetically engineered to overcome death signaling enhance adoptive cancer immunotherapy. J Clin Invest. 2019;129:1551-1565. Oda SK, Anderson KG, Ravikumar P, Bonson P, Garcia NM, Jenkins CM, Zhuang S, Daman AW, Chiu EY, Bates BM, Greenberg, PD. A Fas-4-1BB fusion protein converts a death to a pro-survival signal and enhances T cell therapy. J Exp Med. 2020;217:e20191166. Prior IA, Hood FE, Hartley JL. The frequency of Ras mutations in cancer. Cancer Res. 2020; 80: 2969–2974. Leidner R, Sanjuan Silva N, Huang H, Sprott D, Zheng C, Shih Y-P, Leung A, Payne R, Sutcliffe K, Cramer J, Rosenberg SA, Fox BA, Urba WJ, Tran E. Neoantigen T-cell receptor gene therapy in pancreatic cancer. N Engl J Med. 2022;386, 2112–2119.

Ethics Approval

These studies were approved by Affini-T Therapeutics and Fred Hutchinson Cancer Research Center Ethics Boards, approval number EB17-010-303 and PROTO000050898, respectively.

The widespread regulation of microRNA biogenesis, function and decay.

Abstract: MicroRNAs (miRNAs) are a large family of post-transcriptional regulators of gene expression that are ~21 nucleotides in length and control many developmental and cellular processes in eukaryotic organisms. Research during the past decade has identified major factors participating in miRNA biogenesis and has established basic principles of miRNA function. More recently, it has become apparent that miRNA regulators themselves are subject to sophisticated control. Many reports over the past few years have reported the regulation of miRNA metabolism and function by a range of mechanisms involving numerous protein-protein and protein-RNA interactions. Such regulation has an important role in the context-specific functions of miRNAs.

Causes and consequences of microRNA dysregulation in cancer

Abstract: Over the past several years it has become clear that alterations in the expression of microRNA (miRNA) genes contribute to the pathogenesis of most — if not all — human malignancies. These alterations can be caused by various mechanisms, including deletions, amplifications or mutations involving miRNA loci, epigenetic silencing or the dysregulation of transcription factors that target specific miRNAs. Because malignant cells show dependence on the dysregulated expression of miRNA genes, which in turn control or are controlled by the dysregulation of multiple protein-coding oncogenes or tumour suppressor genes, these small RNAs provide important opportunities for the development of future miRNA-based therapies.

Many roads to maturity: microRNA biogenesis pathways and their regulation

Abstract: MicroRNAs are important regulators of gene expression that control both physiological and pathological processes such as development and cancer. Although their mode of action has attracted great attention, the principles governing their expression and activity are only beginning to emerge. Recent studies have introduced a paradigm shift in our understanding of the microRNA biogenesis pathway, which was previously believed to be universal to all microRNAs. Maturation steps specific to individual microRNAs have been uncovered, and these offer a plethora of regulatory options after transcription with multiple proteins affecting microRNA processing efficiency. Here we review the recent advances in knowledge of the microRNA biosynthesis pathways and discuss their impact on post-transcriptional microRNA regulation during tumour development.

Non-viral vectors for gene-based therapy

Abstract: Gene-based therapy is the intentional modulation of gene expression in specific cells to treat pathological conditions This modulation is accomplished by introducing exogenous nucleic acids such as DNA, mRNA, small interfering RNA (siRNA), microRNA (miRNA) or antisense oligonucleotides Given the large size and the negative charge of these macromolecules, their delivery is typically mediated by carriers or vectors In this Review, we introduce the biological barriers to gene delivery in vivo and discuss recent advances in material sciences, nanotechnology and nucleic acid chemistry that have yielded promising non-viral delivery systems, some of which are currently undergoing testing in clinical trials The diversity of these systems highlights the recent progress of gene-based therapy using non-viral approaches