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1.
Cell ; 187(9): 2269-2287.e16, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38608703

ABSTRACT

Knudson's "two-hit" paradigm posits that carcinogenesis requires inactivation of both copies of an autosomal tumor suppressor gene. Here, we report that the glycolytic metabolite methylglyoxal (MGO) transiently bypasses Knudson's paradigm by inactivating the breast cancer suppressor protein BRCA2 to elicit a cancer-associated, mutational single-base substitution (SBS) signature in nonmalignant mammary cells or patient-derived organoids. Germline monoallelic BRCA2 mutations predispose to these changes. An analogous SBS signature, again without biallelic BRCA2 inactivation, accompanies MGO accumulation and DNA damage in Kras-driven, Brca2-mutant murine pancreatic cancers and human breast cancers. MGO triggers BRCA2 proteolysis, temporarily disabling BRCA2's tumor suppressive functions in DNA repair and replication, causing functional haploinsufficiency. Intermittent MGO exposure incites episodic SBS mutations without permanent BRCA2 inactivation. Thus, a metabolic mechanism wherein MGO-induced BRCA2 haploinsufficiency transiently bypasses Knudson's two-hit requirement could link glycolysis activation by oncogenes, metabolic disorders, or dietary challenges to mutational signatures implicated in cancer evolution.


Subject(s)
BRCA2 Protein , Breast Neoplasms , Glycolysis , Pyruvaldehyde , Animals , BRCA2 Protein/metabolism , BRCA2 Protein/genetics , Mice , Humans , Female , Pyruvaldehyde/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Haploinsufficiency , Pancreatic Neoplasms/metabolism , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/pathology , Mutation , DNA Damage , DNA Repair , Cell Line, Tumor
2.
Hepatol Int ; 17(4): 850-859, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37067675

ABSTRACT

BACKGROUND AND AIMS: Liver transplantation (LT) is the primary curative option for cirrhotic patients with early-stage hepatocellular carcinoma (HCC). However, tumor recurrence occurs in 15-20% of cases with unfavorable prognosis. We have developed a library of T cell receptors (TCRs) specific for different hepatitis B virus (HBV) antigens, restricted by different molecules of human leucocyte antigen (HLA)-class I, to redirect T cells against HBV antigens (Banu in Sci Rep 4:4166, 2014). We further demonstrated that these transiently functional T cells specific for HBV obtained through messenger RNA (mRNA) electroporation can eliminate HCC cells expressing HBV antigens in vitro and in vivo (Kah in J Clin Invest 127:3177-3188, 2017). A phase I clinical trial for patients with HCC recurrence post-liver transplant was conducted to assess the safety, tolerability, and anti-tumor efficacy of transiently functional HBV-TCR T cells. Here, we report the clinical findings with regard to the safety and anti-tumor efficacy of mRNA electroporated HBV-specific TCR-T cells. (ClinicalTrials.gov identifier: NCT02719782). PATIENTS AND METHODS: A total of six patients with HBV-positive recurrent HCC post-liver transplant and HLA-matched to TCR targeting hepatitis B surface antigen (HBsAg) or hepatitis B core antigen (HBcAg) (HLA-A*02:01/HBsAg, HLA-A*11:01/HBcAg, HLA-B*58:01/HBsAg or HLA-C*08:01/HBsAg) were enrolled in this study. The primary objective was to assess the safety of short-lived mRNA electroporated HBV-TCR T cells based on the incidence and severity of the adverse event (AE) graded per National Cancer Institute Common Terminology Criteria for Adverse Events (NCI CTCAE), Version 4.0. The secondary objective was to determine the effectiveness of HBV-TCR T cells as per RECIST 1.1 criteria. Patients were followed up for survival for 2 years post-end of treatment. RESULTS: The median age of the six patients was 35.5 years (range: 28-47). The median number of HBV-TCR T cell infusions administered was 6.5 (range: 4-12). The treatment-related AE included grade 1 pyrexia. This study reported no cytokine release syndrome nor neurotoxicity. One patient remained alive and five were deceased at the time of the data cutoff (30 April 2020). CONCLUSION: This study has demonstrated that multiple infusions of mRNA electroporated HBV-specific TCR T cells were well-tolerated in patients with HBV-positive recurrent HCC post-liver transplant.


Subject(s)
Carcinoma, Hepatocellular , Hepatitis B , Liver Neoplasms , Liver Transplantation , Humans , Adult , Middle Aged , Hepatitis B virus/genetics , Hepatitis B Surface Antigens , Liver Neoplasms/pathology , Hepatitis B Core Antigens/therapeutic use , RNA, Messenger , Neoplasm Recurrence, Local/therapy , Neoplasm Recurrence, Local/complications , Receptors, Antigen, T-Cell/genetics , Hepatitis B/complications
3.
Theranostics ; 13(2): 621-638, 2023.
Article in English | MEDLINE | ID: mdl-36632230

ABSTRACT

Rationale: Metastasis is a complex process with a molecular underpinning that remains unclear. We hypothesize that cargo proteins conducted by extracellular vesicles (EVs) released from tumors may confer growth and metastasis potential on recipient cells. Here, we report that a cytokine-like secreted protein, FAM3C, contributes to late-stage lung tumor progression. Methods: EV protein profiling was conducted with an unbiased proteomic mass spectrometry analysis on non-small cell lung cancer (NSCLC) and normal lung fibroblast cell lines. Expression of FAM3C was confirmed in a panel of NSCLC cell lines, and correlated to the invasive and metastatic potentials. Functional phenotype of endogenous FAM3C and tumor-derived EVs (TDEs) were further investigated using various biological approaches in RNA and protein levels. Metastasis potential of TDEs secreted by FAM3C-overexpressing carcinoma cells was validated in mouse models. Results: Transcriptomic meta-analysis of pan-cancer datasets confirmed the overexpression of FAM3C - a gene encoding for interleukin-like EMT inducer (ILEI) - in NSCLC tumors, with strong association with poor patient prognosis and cancer metastasis. Aberrant expression of FAM3C in lung carcinoma cells enhances cellular transformation and promotes distant lung tumor colonization. In addition, higher FAM3C concentrations were detected in EVs extracted from plasma samples of NSCLC patients compared to those of healthy subjects. More importantly, we defined a hitherto-unknown mode of microenvironmental crosstalk involving FAM3C in EVs, whereby the delivery and uptake of FAM3C via TDEs enhances oncogenic signaling - in recipient cells that phenocopies the cell-endogenous overexpression of FAM3C. The oncogenicity transduced by FAM3C is executed via a novel interaction with the Ras-related protein RalA, triggering the downstream activation of the Src/Stat3 signaling cascade. Conclusions: Our study describes a novel mechanism for FAM3C-driven carcinogenesis and shed light on EV FAM3C as a driver for metastatic lung tumors that could be exploited for cancer therapeutics.


Subject(s)
Carcinogenesis , Carcinoma, Non-Small-Cell Lung , Extracellular Vesicles , Lung Neoplasms , Animals , Humans , Mice , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/secondary , Cell Line, Tumor , Extracellular Vesicles/metabolism , Lung Neoplasms/metabolism , Lung Neoplasms/pathology , Proteomics
4.
Cancers (Basel) ; 14(17)2022 Sep 02.
Article in English | MEDLINE | ID: mdl-36077849

ABSTRACT

IRF4 is a transcription factor in the interferon regulatory factor (IRF) family. Since the discovery of this gene, various research fields including immunology and oncology have highlighted the unique characteristics and the importance of IRF4 in several biological processes that distinguish it from other IRF family members. In normal lymphocyte development and immunity, IRF4 mediates critical immune responses via interactions with upstream signaling pathways, such as the T-cell receptor and B-cell receptor pathways, as well as their binding partners, which are uniquely expressed in each cell type. On the other hand, IRF4 acts as an oncogene in various mature lymphoid neoplasms when abnormally expressed. IRF4 induces several oncogenes, such as MYC, as well as genes that characterize each cell type by utilizing its ability as a master regulator of immunity. IRF4 and its upstream factor NF-κB form a transcriptional regulatory circuit, including feedback and feedforward loops, to maintain the oncogenic transcriptional program in malignant lymphoid cells. In this review article, we provide an overview of the molecular functions of IRF4 in mature lymphoid neoplasms and highlight its upstream and downstream pathways, as well as the regulatory circuits mediated by IRF4.

5.
Leukemia ; 36(9): 2293-2305, 2022 09.
Article in English | MEDLINE | ID: mdl-35908104

ABSTRACT

Adult T-cell leukemia/lymphoma (ATL) is a genetically complex hematological malignancy derived from mature T cells. Using an integrative approach, we previously identified genes recurrently associated with super-enhancers in ATL. One of those genes was TP73, a TP53 family gene; however, the roles and function of TP73 and its super-enhancer in ATL pathogenesis are poorly understood. Our study demonstrates that TP73 is highly activated under the control of a super-enhancer in ATL cells but not in normal T cells or other hematological malignancies examined. Full-length TP73 is required for ATL cell maintenance in vitro and in vivo via the regulation of cell proliferation and DNA damage response pathways. Notably, recurrent deletions of TP73 exons 2-3 were observed in a fraction of primary ATL cases that harbored the super-enhancer, while induction of this deletion in cell lines further increased proliferation and mutational burden. Our study suggests that formation of the TP73 intragenic super-enhancer and genetic deletion are likely sequentially acquired in relation to intracellular state of ATL cells, which leads to functional alteration of TP73 that confers additional clonal advantage.


Subject(s)
Leukemia-Lymphoma, Adult T-Cell , Adult , Cell Proliferation , Exons , Humans , Mutation , Regulatory Sequences, Nucleic Acid
6.
Nat Commun ; 13(1): 2420, 2022 05 03.
Article in English | MEDLINE | ID: mdl-35504924

ABSTRACT

IRF4 is a master regulator of immunity and is also frequently overexpressed in mature lymphoid neoplasms. Here, we demonstrate the oncogenicity of IRF4 in vivo, its potential effects on T-cell development and clonal evolution using a zebrafish model. IRF4-transgenic zebrafish develop aggressive tumors with massive infiltration of abnormal lymphocytes that spread to distal organs. Many late-stage tumors are mono- or oligoclonal, and tumor cells can expand in recipient animals after transplantation, demonstrating their malignancy. Mutation of p53 accelerates tumor onset, increases penetrance, and results in tumor heterogeneity. Surprisingly, single-cell RNA-sequencing reveals that the majority of tumor cells are double-negative T-cells, many of which express tcr-γ that became dominant as the tumors progress, whereas double-positive T-cells are largely diminished. Gene expression and epigenetic profiling demonstrates that gata3, mycb, lrrn1, patl1 and psip1 are specifically activated in tumors, while genes responsible for T-cell differentiation including id3 are repressed. IRF4-driven tumors are sensitive to the BRD inhibitor.


Subject(s)
Lymphoma, T-Cell , Lymphoma , Animals , Cell Differentiation , Clonal Evolution , Lymphoma/genetics , Zebrafish/genetics
7.
Cancer Res ; 82(3): 406-418, 2022 02 01.
Article in English | MEDLINE | ID: mdl-34893510

ABSTRACT

Multiple myeloma is an incurable malignancy with marked clinical and genetic heterogeneity. The cytogenetic abnormality t(4;14) (p16.3;q32.3) confers aggressive behavior in multiple myeloma. Recently, essential oncogenic drivers in a wide range of cancers have been shown to be controlled by super-enhancers (SE). We used chromatin immunoprecipitation sequencing of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs in t(4;14)-translocated multiple myeloma. The histone chaperone HJURP was aberrantly overexpressed in t(4;14)-positive multiple myeloma due to transcriptional activation by a distal SE induced by the histone lysine methyltransferase NSD2. Silencing of HJURP with short hairpin RNA or CRISPR interference of SE function impaired cell viability and led to apoptosis. Conversely, HJURP overexpression promoted cell proliferation and abrogated apoptosis. Mechanistically, the NSD2/BRD4 complex positively coregulated HJURP transcription by binding the promoter and active elements of its SE. In summary, this study introduces SE profiling as an efficient approach to identify new targets and understand molecular pathogenesis in specific subtypes of cancer. Moreover, HJURP could be a valuable therapeutic target in patients with t(4;14)-positive myeloma. SIGNIFICANCE: A super-enhancer screen in t(4;14) multiple myeloma serves to identify genes that promote growth and survival of myeloma cells, which may be evaluated in future studies as therapeutic targets.


Subject(s)
DNA-Binding Proteins/metabolism , Multiple Myeloma/genetics , Cell Line, Tumor , Cell Proliferation , Humans , Multiple Myeloma/mortality , Multiple Myeloma/pathology , Up-Regulation
8.
Hepatol Int ; 15(6): 1402-1412, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34850325

ABSTRACT

BACKGROUND & AIMS: Immunotherapy with hepatitis B virus (HBV)-specific TCR redirected T (HBV-TCR-T) cells in HBV-related hepatocellular carcinoma (HBV-HCC) patients after liver transplantation was reported to be safe and had potential therapeutic efficacy. We aim to investigate the safety of HBV-TCR-T-cell immunotherapy in advanced HBV-HCC patients who had not met the criteria for liver transplantation. METHODS: We enrolled eight patients with advanced HBV-HCC and adoptively transferred short-lived autologous T cells expressing HBV-specific TCR to perform an open-label, phase 1 dose-escalation study (NCT03899415). The primary endpoint was to evaluate the safety of HBV-TCR-T-cell therapy according to National Cancer Institute Common Terminology Criteria for Adverse Events (version 4.03) during the dose-escalation process. The secondary endpoint was to assess the efficacy of HBV-TCR-T-cell therapy by evaluating the anti-tumor responses using RECIST criteria (version 1.1) and the overall survival. RESULTS: Adverse events were observed in two participants among the 8 patients enrolled. Only one patient experienced a Grade 3 liver-related adverse event after receiving a dose of 1 × 105 HBV-TCR-T cells/kg, then normalized without interventions with immunosuppressive agents. Among the patients, one achieved a partial response lasting for 27.7 months. Importantly, most of the patients exhibited a reduction or stabilization of circulating HBsAg and HBV DNA levels after HBV-TCR-T-cell infusion, indicating the on-target effects. CONCLUSIONS: The adoptive transfer of HBV-TCR-T cells into advanced HBV-HCC patients were generally safe and well-tolerated. Observations of clinical efficacy support the continued development and eventual application of this treatment strategy in patients with advanced HBV-related HCC. CLINICAL TRIALS REGISTRATION: This study was registered at ClinicalTrials.gov (NCT03899415).


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Carcinoma, Hepatocellular/therapy , Hepatitis B virus , Humans , Immunotherapy , Liver Neoplasms/therapy , Receptors, Antigen, T-Cell , T-Lymphocytes
9.
Immunity ; 54(8): 1883-1900.e5, 2021 08 10.
Article in English | MEDLINE | ID: mdl-34331874

ABSTRACT

Mononuclear phagocytes (MNPs) encompass dendritic cells, monocytes, and macrophages (MoMac), which exhibit antimicrobial, homeostatic, and immunoregulatory functions. We integrated 178,651 MNPs from 13 tissues across 41 datasets to generate a MNP single-cell RNA compendium (MNP-VERSE), a publicly available tool to map MNPs and define conserved gene signatures of MNP populations. Next, we generated a MoMac-focused compendium that revealed an array of specialized cell subsets widely distributed across multiple tissues. Specific pathological forms were expanded in cancer and inflammation. All neoplastic tissues contained conserved tumor-associated macrophage populations. In particular, we focused on IL4I1+CD274(PD-L1)+IDO1+ macrophages, which accumulated in the tumor periphery in a T cell-dependent manner via interferon-γ (IFN-γ) and CD40/CD40L-induced maturation from IFN-primed monocytes. IL4I1_Macs exhibited immunosuppressive characteristics through tryptophan degradation and promoted the entry of regulatory T cell into tumors. This integrated analysis provides a robust online-available platform for uniform annotation and dissection of specific macrophage functions in healthy and pathological states.


Subject(s)
Dendritic Cells/immunology , Gene Expression/immunology , Monocytes/immunology , Transcriptome/genetics , Tumor-Associated Macrophages/immunology , Arthritis, Rheumatoid/immunology , COVID-19/immunology , Gene Expression/genetics , Gene Expression Profiling , Humans , Interferon-gamma/immunology , L-Amino Acid Oxidase/metabolism , Liver Cirrhosis/immunology , Macrophages/immunology , Neoplasms/immunology , RNA, Small Cytoplasmic/genetics , Single-Cell Analysis , T-Lymphocytes, Regulatory/immunology , Transcriptome/immunology
10.
Cell ; 184(13): 3394-3409.e20, 2021 06 24.
Article in English | MEDLINE | ID: mdl-34077752

ABSTRACT

The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.


Subject(s)
Bacteria/metabolism , Embryonic Development , Fetus/cytology , Fetus/microbiology , Leukocytes/cytology , Adult , Bacteria/genetics , Bacteria/ultrastructure , Cell Proliferation , Dendritic Cells/metabolism , Female , Fetus/ultrastructure , Gastrointestinal Tract/embryology , Gastrointestinal Tract/ultrastructure , Humans , Immunologic Memory , Lymphocyte Activation/immunology , Microbial Viability , Pregnancy , Pregnancy Trimester, Second , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Reproducibility of Results , T-Lymphocytes/cytology
11.
Blood Cancer J ; 11(2): 32, 2021 02 12.
Article in English | MEDLINE | ID: mdl-33579893

ABSTRACT

Multiple myeloma (MM) is an aggressive plasma cell neoplasm characterized by genomic heterogeneity. Superenhancers (SEs) are defined as large clusters of enhancers in close genomic proximity, which regulate genes for maintaining cellular identity and promote oncogenic transcription to which cancer cells highly addicted. Here, we analyzed cis-regulatory elements in MM samples with H3K27ac ChIP-seq, to identify novel SE-associated genes involved in the myeloma pathogenesis. SEs and their associated genes in cancerous tissue were compared with the control samples, and we found SE analysis alone uncovered cell-lineage-specific transcription factors and well-known oncogenes ST3GAL6 and ADM. Using a transcriptional CDK7 inhibitor, THZ1, coupled with H3K27ac ChlP-seq, we identified MAGI2 as a novel SE-associated gene of myeloma cells. Elevated MAGI2 was related to myelomagenesis with gradual increased expression from MGUS, SMM to newly diagnosed and relapsed MM. High prevalence of MAGI2 was also associated with poor survival of MM patients. Importantly, inhibition of the SE activity associated with MAGI2 decreased MAGI2 expression, inhibited cell growth and induced cell apoptosis. Mechanistically, we revealed that the oncogenic transcription factor, MAF, directly bound to the SE region and activated gene transcription. In summary, the discoveries of these acquired SEs-associated genes and the novel mechanism by which they are regulated provide new insights into MM biology and MAGI2-MAF-SE regulatory circuit offer potential novel targets for disease treatment.


Subject(s)
Gene Expression Regulation, Neoplastic , Multiple Myeloma/genetics , Adaptor Proteins, Signal Transducing/genetics , Cell Line, Tumor , Enhancer Elements, Genetic , Gene Regulatory Networks , Guanylate Kinases/genetics , Humans , Multiple Myeloma/pathology , Oncogenes , Proto-Oncogene Proteins c-maf/genetics
12.
Cell ; 183(2): 377-394.e21, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32976798

ABSTRACT

We employed scRNA sequencing to extensively characterize the cellular landscape of human liver from development to disease. Analysis of ∼212,000 cells representing human fetal, hepatocellular carcinoma (HCC), and mouse liver revealed remarkable fetal-like reprogramming of the tumor microenvironment. Specifically, the HCC ecosystem displayed features reminiscent of fetal development, including re-emergence of fetal-associated endothelial cells (PLVAP/VEGFR2) and fetal-like (FOLR2) tumor-associated macrophages. In a cross-species comparative analysis, we discovered remarkable similarity between mouse embryonic, fetal-liver, and tumor macrophages. Spatial transcriptomics further revealed a shared onco-fetal ecosystem between fetal liver and HCC. Furthermore, gene regulatory analysis, spatial transcriptomics, and in vitro functional assays implicated VEGF and NOTCH signaling in maintaining onco-fetal ecosystem. Taken together, we report a shared immunosuppressive onco-fetal ecosystem in fetal liver and HCC. Our results unravel a previously unexplored onco-fetal reprogramming of the tumor ecosystem, provide novel targets for therapeutic interventions in HCC, and open avenues for identifying similar paradigms in other cancers and disease.


Subject(s)
Carcinoma, Hepatocellular/pathology , Endothelial Cells/metabolism , Tumor Microenvironment/genetics , Adult , Animals , Carcinoma, Hepatocellular/genetics , Cell Line , Disease Models, Animal , Endothelial Cells/pathology , Female , Folate Receptor 2/metabolism , Gene Expression Profiling/methods , Humans , Liver/pathology , Liver Neoplasms/genetics , Macrophages/metabolism , Male , Membrane Proteins/metabolism , Mice , Receptors, Notch/genetics , Receptors, Notch/metabolism , Signal Transduction/genetics , Transcriptome/genetics , Vascular Endothelial Growth Factor Receptor-2/metabolism
13.
Elife ; 92020 08 03.
Article in English | MEDLINE | ID: mdl-32744504

ABSTRACT

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin+ cells, in a manner independent of the nearby TF FOXA2. One-by-one disruption of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.


Subject(s)
Cell Differentiation/physiology , Islets of Langerhans/cytology , RNA, Long Noncoding/physiology , CRISPR-Cas Systems , Cells, Cultured , Gene Deletion , Gene Expression Regulation, Developmental , Gene Knockout Techniques , HEK293 Cells , Human Embryonic Stem Cells , Humans , Islets of Langerhans/embryology , Male , Protein Biosynthesis , RNA, Long Noncoding/genetics , Transcription Factors/metabolism
14.
J Indian Inst Sci ; 100(3): 579-588, 2020.
Article in English | MEDLINE | ID: mdl-32837038

ABSTRACT

Tumors exhibit genetic and phenotypic diversity leading to intra-tumor heterogeneity (ITH). Further complex ecosystem (stromal and immune cells) of tumors contributes into the ITH. This ITH allows tumors to overcome various selection pressures such as anti-cancer therapies and metastasis at distant organs. Single-cell RNA-seq (scRNA-seq) has provided unprecedented insights into ITH and its implications in drug resistance and metastasis. As scRNA-seq technology grows and provides many new findings, new tools on different programming platforms are frequently generated. Here, we aim to provide a framework and guidelines for new entrants into the field of scRNA-seq. In this review, we discuss the current state-of-art of scRNA-seq analysis step-by-step including filtering, normalization and analysis. First, we discuss the brief history of experimental methods, followed by data processing and implications in precision oncology.

15.
Blood ; 135(12): 934-947, 2020 03 19.
Article in English | MEDLINE | ID: mdl-31972002

ABSTRACT

Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive hematological malignancy derived from mature CD4+ T-lymphocytes. Here, we demonstrate the transcriptional regulatory network driven by 2 oncogenic transcription factors, IRF4 and NF-κB, in ATL cells. Gene expression profiling of primary ATL samples demonstrated that the IRF4 gene was more highly expressed in ATL cells than in normal T cells. Chromatin immunoprecipitation sequencing analysis revealed that IRF4-bound regions were more frequently found in super-enhancers than in typical enhancers. NF-κB was found to co-occupy IRF4-bound regulatory elements and formed a coherent feed-forward loop to coordinately regulate genes involved in T-cell functions and development. Importantly, IRF4 and NF-κB regulated several cancer genes associated with super-enhancers in ATL cells, including MYC, CCR4, and BIRC3. Genetic inhibition of BIRC3 induced growth inhibition in ATL cells, implicating its role as a critical effector molecule downstream of the IRF4-NF-κB transcriptional network.


Subject(s)
Interferon Regulatory Factors/metabolism , Leukemia-Lymphoma, Adult T-Cell/etiology , Leukemia-Lymphoma, Adult T-Cell/metabolism , NF-kappa B/metabolism , Signal Transduction , Apoptosis/genetics , Baculoviral IAP Repeat-Containing 3 Protein/metabolism , Cell Line, Tumor , Cell Proliferation , Cell Survival/genetics , Computational Biology , Gene Expression Profiling , Gene Knockdown Techniques , Humans , Models, Biological , RNA, Small Interfering/genetics , Receptors, CCR4/metabolism
16.
Molecules ; 23(5)2018 May 02.
Article in English | MEDLINE | ID: mdl-29724031

ABSTRACT

Cancer cells are highly reliant on certain molecular pathways, which support their survival and proliferation. The fundamental concept of molecularly targeted therapy is to target a protein that is specifically deregulated or overexpressed in cancer cells. However, drug resistance and tumor heterogeneity are major obstacles in the development of specific inhibitors. Additionally, many driver oncogenes exert their oncogenic property via abnormal expression without having genetic mutations. Interestingly, recent accumulating evidence has demonstrated that many critical cancer genes are driven by a unique class of enhancers termed super-enhancers. Genes associated with super-enhancers are relatively more susceptible to the inhibition of general transcriptional machinery compared with genes that are regulated by typical enhancers. Cancer cells are more sensitive to treatment with small-molecule inhibitors of CDK7 or BRD4 than non-transformed cells. These findings proposed a novel strategy to identify functionally important genes as well as novel therapeutic modalities in cancer. This approach would be particularly useful for genetically complicated cancers, such as adult T-cell leukemia (ATL), whereby a large mutational burden is present, but the functional consequences of each mutation have not been well-studied. In this review, we discuss recent findings on super-enhancers, underlying mechanisms, and the efficacy of small-molecule transcriptional inhibitors in ATL.


Subject(s)
Antineoplastic Agents/therapeutic use , Cyclin-Dependent Kinase 4/antagonists & inhibitors , Leukemia-Lymphoma, Adult T-Cell/drug therapy , Neoplasm Proteins/antagonists & inhibitors , Nuclear Proteins/antagonists & inhibitors , Transcription Factors/antagonists & inhibitors , Transcription, Genetic/drug effects , Animals , Antineoplastic Agents/chemistry , Cell Cycle Proteins , Cyclin-Dependent Kinase 4/genetics , Cyclin-Dependent Kinase 4/metabolism , Humans , Leukemia-Lymphoma, Adult T-Cell/genetics , Leukemia-Lymphoma, Adult T-Cell/metabolism , Leukemia-Lymphoma, Adult T-Cell/pathology , Neoplasm Proteins/biosynthesis , Neoplasm Proteins/genetics , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
17.
Blood ; 130(21): 2326-2338, 2017 11 23.
Article in English | MEDLINE | ID: mdl-28978570

ABSTRACT

A number of studies have recently demonstrated that super-enhancers, which are large cluster of enhancers typically marked by a high level of acetylation of histone H3 lysine 27 and mediator bindings, are frequently associated with genes that control and define cell identity during normal development. Super-enhancers are also often enriched at cancer genes in various malignancies. The identification of such enhancers would pinpoint critical factors that directly contribute to pathogenesis. In this study, we performed enhancer profiling using primary leukemia samples from adult T-cell leukemia/lymphoma (ATL), which is a genetically heterogeneous intractable cancer. Super-enhancers were enriched at genes involved in the T-cell activation pathway, including IL2RA/CD25, CD30, and FYN, in both ATL and normal mature T cells, which reflected the origin of the leukemic cells. Super-enhancers were found at several known cancer gene loci, including CCR4, PIK3R1, and TP73, in multiple ATL samples, but not in normal mature T cells, which implicated those genes in ATL pathogenesis. A small-molecule CDK7 inhibitor, THZ1, efficiently inhibited cell growth, induced apoptosis, and downregulated the expression of super-enhancer-associated genes in ATL cells. Furthermore, enhancer profiling combined with gene expression analysis identified a previously uncharacterized gene, TIAM2, that was associated with super-enhancers in all ATL samples, but not in normal T cells. Knockdown of TIAM2 induced apoptosis in ATL cell lines, whereas overexpression of this gene promoted cell growth. Our study provides a novel strategy for identifying critical cancer genes.


Subject(s)
Enhancer Elements, Genetic/genetics , Gene Expression Profiling , Genes, Neoplasm , Leukemia-Lymphoma, Adult T-Cell/genetics , Cell Line, Tumor , Cell Proliferation/drug effects , Cell Survival/drug effects , Cell Survival/genetics , Cyclin-Dependent Kinases/antagonists & inhibitors , Cyclin-Dependent Kinases/metabolism , Down-Regulation/drug effects , Down-Regulation/genetics , Gene Expression Regulation, Leukemic/drug effects , Genetic Association Studies , Humans , Leukemia-Lymphoma, Adult T-Cell/drug therapy , Leukemia-Lymphoma, Adult T-Cell/immunology , Leukemia-Lymphoma, Adult T-Cell/pathology , Lymphocyte Activation/genetics , Phenylenediamines/pharmacology , Phenylenediamines/therapeutic use , Phosphorylation/drug effects , Protein Kinase Inhibitors/pharmacology , Pyrimidines/pharmacology , Pyrimidines/therapeutic use , RNA Polymerase II/metabolism , T-Lymphocytes/drug effects , T-Lymphocytes/metabolism , Cyclin-Dependent Kinase-Activating Kinase
18.
Biochem Biophys Res Commun ; 433(1): 40-6, 2013 Mar 29.
Article in English | MEDLINE | ID: mdl-23454121

ABSTRACT

Thioredoxin interacting protein (TXNIP), first identified as an inhibitor of thioredoxin, is also a tumor suppressor as well as an inhibitor of lipogenesis. TXNIP is known to be transcriptionally regulated in response to nutrients such as glucose and stress signals, including endoplasmic reticulum stress and lactic acidosis. In this study, we characterized the transcriptional regulation of TXNIP in response to hypoxia. Using a hepatocellular carcinoma cell line, we have found that TXNIP mRNA expression is regulated in a biphasic manner in hypoxia whereby TXNIP expression showed an initial rapid decrease, followed by an increase under prolonged hypoxia. Interestingly, we have shown that TXNIP induction in prolonged hypoxia is independent of the Hypoxia-Inducible Factor (HIF) transcription factor. The effect of hypoxia on TXNIP expression is mediated via the inhibition of the 4E-BP1/eIF4E axis of mechanistic target of rapamycin (mTORC1). Thus, we found that inhibiting mTORC1-dependent 4E-BP1 phosphorylation mimics the effect of hypoxia on TXNIP expression. Furthermore, overexpressing eIF4E prevents the induction of TXNIP in hypoxia. Our results suggest that mTORC1 may be an important regulator of hypoxia-dependent gene expression.


Subject(s)
Carrier Proteins/genetics , Cell Hypoxia/genetics , Cell Hypoxia/physiology , TOR Serine-Threonine Kinases/metabolism , Thioredoxins/genetics , Adaptor Proteins, Signal Transducing/antagonists & inhibitors , Animals , Aryl Hydrocarbon Receptor Nuclear Translocator/antagonists & inhibitors , Aryl Hydrocarbon Receptor Nuclear Translocator/genetics , Aryl Hydrocarbon Receptor Nuclear Translocator/metabolism , Base Sequence , Carrier Proteins/antagonists & inhibitors , Carrier Proteins/biosynthesis , Cell Cycle Proteins , Enzyme Inhibitors/pharmacology , Eukaryotic Initiation Factors , Gene Expression Regulation/drug effects , HEK293 Cells , Hep G2 Cells , Humans , Mechanistic Target of Rapamycin Complex 1 , Mice , Multiprotein Complexes , NIH 3T3 Cells , Phosphoproteins/antagonists & inhibitors , Procollagen-Proline Dioxygenase/antagonists & inhibitors , Proteins/metabolism , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Small Interfering/genetics , Thioredoxins/biosynthesis , Transcription, Genetic
19.
Int J Mol Imaging ; 2011: 942063, 2011.
Article in English | MEDLINE | ID: mdl-21966591

ABSTRACT

Purpose. The aims were to correlate individual marrow metabolic changes after chemotherapy with bone marrow biopsy (BMBx) for its potential value of personalized care in lymphoma. Methods. 26 patients (mean age, 58 ± 15 y; 13 female, 13 male) with follicular lymphoma or diffuse large B-cell lymphoma, referred to FDG-PET/CT imaging, who had BMBx from unilateral or bilateral iliac crest(s) before chemotherapy, were studied retrospectively. The maximal standardized uptake value (SUV) was measured from BMBx site over the same area on both initial staging and first available restaging FDG-PET/CT scan. Results. 35 BMBx sites in 26 patients were evaluated. 12 of 35 sites were BMBx positive with interval decrease in SUV in 11 of 12 sites (92%). The remaining 23 of 35 sites were BMBx negative with interval increase in SUV in 21 of 23 sites (91%). The correlation between SUV change over the BMBx site before and after chemotherapy and BMBx result was significant (P < 0.0001). Conclusions. This preliminary result demonstrates a strong correlation between marrow metabolic changes (as determined by FDG PET) after chemotherapy and bone marrow involvement proven by biopsy. This may provide a retrospective means of personalized management of marrow involvement in deciding whether to deliver more extended therapy or closer followup of lymphoma patients.

20.
Mol Imaging Biol ; 11(5): 296-302, 2009.
Article in English | MEDLINE | ID: mdl-19430847

ABSTRACT

PURPOSE: The aim of this study was to correlate metabolic behavior of follicular lymphoma with proliferative index (Ki67). MATERIALS AND METHODS: Pre-treatment 2-deoxy-2-[F-18]fluoro-D-glucose positron emission tomography-computed tomography scans of 23 patients with pathologic diagnosis of follicular lymphoma were retrospectively analyzed together with Ki67. The maximal standardized uptake value (SUV) was measured and corrected to glucose level of 100 mg/dl over the biopsy region (BxSUV100) and at the highest tumor activity of the body (BmSUV100). RESULTS: BxSUV100 was significantly correlated with Ki67 (p = 0.037). There was an increasing trend of metabolic activity across the pathologic grades of follicular lymphomas. BmSUV100 and BxSUV100 were also significantly different (p < 0.0005), suggesting potential pitfalls of sampling error by histology. CONCLUSION: The increasing trend of metabolic activity across follicular lymphoma grades correlates with cellular proliferation. The metabolic information from positron emission tomography-computed tomography may offer another useful parameter in the management of follicular lymphomas.


Subject(s)
Lymphoma, Follicular/metabolism , Lymphoma, Follicular/pathology , Biopsy , Cell Growth Processes/physiology , Fluorodeoxyglucose F18/metabolism , Humans , Ki-67 Antigen/biosynthesis , Lymphoma, Follicular/diagnostic imaging , Positron-Emission Tomography/methods , Retrospective Studies , Whole Body Imaging
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