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Kundu M, Butti R, Panda VK, Malhotra D, Das S, Mitra T, Kapse P, Gosavi SW, Kundu GC. Modulation of the tumor microenvironment and mechanism of immunotherapy-based drug resistance in breast cancer. Mol Cancer 2024; 23:92. [PMID: 38715072 PMCID: PMC11075356 DOI: 10.1186/s12943-024-01990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024] Open
Abstract
Breast cancer, the most frequent female malignancy, is often curable when detected at an early stage. The treatment of metastatic breast cancer is more challenging and may be unresponsive to conventional therapy. Immunotherapy is crucial for treating metastatic breast cancer, but its resistance is a major limitation. The tumor microenvironment (TME) is vital in modulating the immunotherapy response. Various tumor microenvironmental components, such as cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), and myeloid-derived suppressor cells (MDSCs), are involved in TME modulation to cause immunotherapy resistance. This review highlights the role of stromal cells in modulating the breast tumor microenvironment, including the involvement of CAF-TAM interaction, alteration of tumor metabolism leading to immunotherapy failure, and other latest strategies, including high throughput genomic screening, single-cell and spatial omics techniques for identifying tumor immune genes regulating immunotherapy response. This review emphasizes the therapeutic approach to overcome breast cancer immune resistance through CAF reprogramming, modulation of TAM polarization, tumor metabolism, and genomic alterations.
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Affiliation(s)
- Moumita Kundu
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, India
- Department of Pharmaceutical Technology, Brainware University, West Bengal, 700125, India
| | - Ramesh Butti
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75235, USA
| | - Venketesh K Panda
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, India
| | - Diksha Malhotra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, India
| | - Sumit Das
- National Centre for Cell Sciences, Savitribai Phule Pune University Campus, Pune, 411007, India
| | - Tandrima Mitra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, India
| | - Prachi Kapse
- School of Basic Medical Sciences, Savitribai Phule Pune University, Pune, 411007, India
| | - Suresh W Gosavi
- School of Basic Medical Sciences, Savitribai Phule Pune University, Pune, 411007, India
| | - Gopal C Kundu
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, 751024, India.
- Kalinga Institute of Medical Sciences (KIMS), KIIT Deemed to be University, Bhubaneswar, 751024, India.
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Kong R, Wang N, Zhou CL, Lu J. Prognostic Value of an Immune Long Non-Coding RNA Signature in Liver Hepatocellular Carcinoma. J Microbiol Biotechnol 2024; 34:958-968. [PMID: 38494878 DOI: 10.4014/jmb.2308.08022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 03/19/2024]
Abstract
In recent years, there has been a growing recognition of the important role that long non-coding RNAs (lncRNAs) play in the immunological process of hepatocellular carcinoma (LIHC). An increasing number of studies have shown that certain lncRNAs hold great potential as viable options for diagnosis and treatment in clinical practice. The primary objective of our investigation was to devise an immune lncRNA profile to explore the significance of immune-associated lncRNAs in the accurate diagnosis and prognosis of LIHC. Gene expression profiles of LIHC samples obtained from TCGA database were screened for immune-related genes. The optimal immune-related lncRNA signature was built via correlational analysis, univariate and multivariate Cox analysis. Then, the Kaplan-Meier plot, ROC curve, clinical analysis, gene set enrichment analysis, and principal component analysis were performed to evaluate the capability of the immune lncRNA signature as a prognostic indicator. Six long non-coding RNAs were identified via correlation analysis and Cox regression analysis considering their interactions with immune genes. Subsequently, tumor samples were categorized into two distinct risk groups based on different clinical outcomes. Stratification analysis indicated that the prognostic ability of this signature acted as an independent factor. The Kaplan-Meier method was employed to conduct survival analysis, results showed a significant difference between the two risk groups. The predictive performance of this signature was validated by principal component analysis (PCA). Additionally, data obtained from gene set enrichment analysis (GSEA) revealed several potential biological processes in which these biomarkers may be involved. To summarize, this study demonstrated that this six-lncRNA signature could be identified as a potential factor that can independently predict the prognosis of LIHC patients.
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Affiliation(s)
- Rui Kong
- Department of Gastroenterology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, P.R. China
| | - Nan Wang
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Chun Li Zhou
- Department of Gastroenterology, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, P.R. China
| | - Jie Lu
- Department of Gastroenterology, Pu Dong Area Gongli Hospital, School of Medicine, Shanghai University, Shanghai 200135, P.R. China
- Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
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Olszewska M, Malcher A, Stokowy T, Pollock N, Berman AJ, Budkiewicz S, Kamieniczna M, Jackowiak H, Suszynska-Zajczyk J, Jedrzejczak P, Yatsenko AN, Kurpisz M. Effects of Tcte1 knockout on energy chain transportation and spermatogenesis: implications for male infertility. Hum Reprod Open 2024; 2024:hoae020. [PMID: 38650655 PMCID: PMC11035007 DOI: 10.1093/hropen/hoae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/08/2024] [Indexed: 04/25/2024] Open
Abstract
STUDY QUESTION Is the Tcte1 mutation causative for male infertility? SUMMARY ANSWER Our collected data underline the complex and devastating effect of the single-gene mutation on the testicular molecular network, leading to male reproductive failure. WHAT IS KNOWN ALREADY Recent data have revealed mutations in genes related to axonemal dynein arms as causative for morphology and motility abnormalities in spermatozoa of infertile males, including dysplasia of fibrous sheath (DFS) and multiple morphological abnormalities in the sperm flagella (MMAF). The nexin-dynein regulatory complex (N-DRC) coordinates the dynein arm activity and is built from the DRC1-DRC7 proteins. DRC5 (TCTE1), one of the N-DRC elements, has already been reported as a candidate for abnormal sperm flagella beating; however, only in a restricted manner with no clear explanation of respective observations. STUDY DESIGN SIZE DURATION Using the CRISPR/Cas9 genome editing technique, a mouse Tcte1 gene knockout line was created on the basis of the C57Bl/6J strain. The mouse reproductive potential, semen characteristics, testicular gene expression levels, sperm ATP, and testis apoptosis level measurements were then assessed, followed by visualization of N-DRC proteins in sperm, and protein modeling in silico. Also, a pilot genomic sequencing study of samples from human infertile males (n = 248) was applied for screening of TCTE1 variants. PARTICIPANTS/MATERIALS SETTING METHODS To check the reproductive potential of KO mice, adult animals were crossed for delivery of three litters per caged pair, but for no longer than for 6 months, in various combinations of zygosity. All experiments were performed for wild-type (WT, control group), heterozygous Tcte1+/- and homozygous Tcte1-/- male mice. Gross anatomy was performed on testis and epididymis samples, followed by semen analysis. Sequencing of RNA (RNAseq; Illumina) was done for mice testis tissues. STRING interactions were checked for protein-protein interactions, based on changed expression levels of corresponding genes identified in the mouse testis RNAseq experiments. Immunofluorescence in situ staining was performed to detect the N-DRC complex proteins: Tcte1 (Drc5), Drc7, Fbxl13 (Drc6), and Eps8l1 (Drc3) in mouse spermatozoa. To determine the amount of ATP in spermatozoa, the luminescence level was measured. In addition, immunofluorescence in situ staining was performed to check the level of apoptosis via caspase 3 visualization on mouse testis samples. DNA from whole blood samples of infertile males (n = 137 with non-obstructive azoospermia or cryptozoospermia, n = 111 samples with a spectrum of oligoasthenoteratozoospermia, including n = 47 with asthenozoospermia) was extracted to perform genomic sequencing (WGS, WES, or Sanger). Protein prediction modeling of human-identified variants and the exon 3 structure deleted in the mouse knockout was also performed. MAIN RESULTS AND THE ROLE OF CHANCE No progeny at all was found for the homozygous males which were revealed to have oligoasthenoteratozoospermia, while heterozygous animals were fertile but manifested oligozoospermia, suggesting haploinsufficiency. RNA-sequencing of the testicular tissue showed the influence of Tcte1 mutations on the expression pattern of 21 genes responsible for mitochondrial ATP processing or linked with apoptosis or spermatogenesis. In Tcte1-/- males, the protein was revealed in only residual amounts in the sperm head nucleus and was not transported to the sperm flagella, as were other N-DRC components. Decreased ATP levels (2.4-fold lower) were found in the spermatozoa of homozygous mice, together with disturbed tail:midpiece ratios, leading to abnormal sperm tail beating. Casp3-positive signals (indicating apoptosis) were observed in spermatogonia only, at a similar level in all three mouse genotypes. Mutation screening of human infertile males revealed one novel and five ultra-rare heterogeneous variants (predicted as disease-causing) in 6.05% of the patients studied. Protein prediction modeling of identified variants revealed changes in the protein surface charge potential, leading to disruption in helix flexibility or its dynamics, thus suggesting disrupted interactions of TCTE1 with its binding partners located within the axoneme. LARGE SCALE DATA All data generated or analyzed during this study are included in this published article and its supplementary information files. RNAseq data are available in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE207805. The results described in the publication are based on whole-genome or exome sequencing data which includes sensitive information in the form of patient-specific germline variants. Information regarding such variants must not be shared publicly following European Union legislation, therefore access to raw data that support the findings of this study are available from the corresponding author upon reasonable request. LIMITATIONS REASONS FOR CAUTION In the study, the in vitro fertilization performance of sperm from homozygous male mice was not checked. WIDER IMPLICATIONS OF THE FINDINGS This study contains novel and comprehensive data concerning the role of TCTE1 in male infertility. The TCTE1 gene is the next one that should be added to the 'male infertility list' because of its crucial role in spermatogenesis and proper sperm functioning. STUDY FUNDING/COMPETING INTERESTS This work was supported by National Science Centre in Poland, grants no.: 2015/17/B/NZ2/01157 and 2020/37/B/NZ5/00549 (to M.K.), 2017/26/D/NZ5/00789 (to A.M.), and HD096723, GM127569-03, NIH SAP #4100085736 PA DoH (to A.N.Y.). The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.
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Affiliation(s)
- Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Agnieszka Malcher
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Stokowy
- Scientific Computing Group, IT Division, University of Bergen, Bergen, Norway
| | - Nijole Pollock
- Department of OB/GYN and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrea J Berman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sylwia Budkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Hanna Jackowiak
- Department of Histology and Embryology, Poznan University of Life Sciences, Poznan, Poland
| | | | - Piotr Jedrzejczak
- Division of Infertility and Reproductive Endocrinology, Department of Gynecology, Obstetrics and Gynecological Oncology, Poznan University of Medical Sciences, Poznan, Poland
| | - Alexander N Yatsenko
- Department of OB/GYN and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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Naik A, Lattab B, Qasem H, Decock J. Cancer testis antigens: Emerging therapeutic targets leveraging genomic instability in cancer. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200768. [PMID: 38596293 PMCID: PMC10876628 DOI: 10.1016/j.omton.2024.200768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Cancer care has witnessed remarkable progress in recent decades, with a wide array of targeted therapies and immune-based interventions being added to the traditional treatment options such as surgery, chemotherapy, and radiotherapy. However, despite these advancements, the challenge of achieving high tumor specificity while minimizing adverse side effects continues to dictate the benefit-risk balance of cancer therapy, guiding clinical decision making. As such, the targeting of cancer testis antigens (CTAs) offers exciting new opportunities for therapeutic intervention of cancer since they display highly tumor specific expression patterns, natural immunogenicity and play pivotal roles in various biological processes that are critical for tumor cellular fitness. In this review, we delve deeper into how CTAs contribute to the regulation and maintenance of genomic integrity in cancer, and how these mechanisms can be exploited to specifically target and eradicate tumor cells. We review the current clinical trials targeting aforementioned CTAs, highlight promising pre-clinical data and discuss current challenges and future perspectives for future development of CTA-based strategies that exploit tumor genomic instability.
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Affiliation(s)
- Adviti Naik
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Boucif Lattab
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Hanan Qasem
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Julie Decock
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences (CHLS), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Doha, Qatar
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5
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Cho JW, Cao J, Hemberg M. Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution. Genome Biol 2024; 25:65. [PMID: 38459554 PMCID: PMC10921788 DOI: 10.1186/s13059-024-03201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to study both mutational and transcriptomic profiles, but as most studies have been conducted on model systems, little is known about cancer evolution in human patients. Hence, a better understanding of cancer evolution could have important implications for treatment strategies. RESULTS Here, we analyze cancer evolution and clonal selection by jointly considering mutational and transcriptomic profiles of single cells acquired from tumor biopsies from 49 lung cancer samples and 51 samples with chronic myeloid leukemia. Comparing the two profiles, we find that each clone is associated with a preferred transcriptional state. For metastasis and drug resistance, we find that the number of mutations affecting related genes increases as the clone evolves, while changes in gene expression profiles are limited. Surprisingly, we find that mutations affecting ligand-receptor interactions with the tumor microenvironment frequently emerge as clones acquire drug resistance. CONCLUSIONS Our results show that lung cancer and chronic myeloid leukemia maintain a high clonal and transcriptional diversity, and we find little evidence in favor of clonal sweeps. This suggests that for these cancers selection based solely on growth rate is unlikely to be the dominating driving force during cancer evolution.
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Affiliation(s)
- Jae-Won Cho
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jingyi Cao
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Hemberg
- The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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6
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Pugacheva EM, Bhatt DN, Rivero-Hinojosa S, Tajmul M, Fedida L, Price E, Ji Y, Loukinov D, Strunnikov AV, Ren B, Lobanenkov VV. BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome Biol 2024; 25:40. [PMID: 38297316 PMCID: PMC10832218 DOI: 10.1186/s13059-024-03175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters. RESULTS Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements. CONCLUSIONS Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Dharmendra Nath Bhatt
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Md Tajmul
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liron Fedida
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emma Price
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yon Ji
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, Center for Epigenomics, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, 92093-0653, USA
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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Carter JA, Matta B, Battaglia J, Somerville C, Harris BD, LaPan M, Atwal GS, Barnes BJ. Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a-based and Siglece-based vaccination induces antitumor immunity and inhibits metastasis. J Immunother Cancer 2023; 11:e007935. [PMID: 38135347 DOI: 10.1136/jitc-2023-007935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Cancer-testis (CT) genes are targets for tumor antigen-specific immunotherapy given that their expression is normally restricted to the immune-privileged testis in healthy individuals with aberrant expression in tumor tissues. While they represent targetable germ tissue antigens and play important functional roles in tumorigenesis, there is currently no standardized approach for identifying clinically relevant CT genes. Optimized algorithms and validated methods for accurate prediction of reliable CT antigens (CTAs) with high immunogenicity are also lacking. METHODS Sequencing data from the Genotype-Tissue Expression (GTEx) and The Genomic Data Commons (GDC) databases was used for the development of a bioinformatic pipeline to identify CT exclusive genes. A CT germness score was calculated based on the number of CT genes expressed within a tumor type and their degree of expression. The impact of tumor germness on clinical outcome was evaluated using healthy GTEx and GDC tumor samples. We then used a triple-negative breast cancer mouse model to develop and test an algorithm that predicts epitope immunogenicity based on the identification of germline sequences with strong major histocompatibility complex class I (MHCI) and MHCII binding affinities. Germline sequences for CT genes were synthesized as long synthetic peptide vaccines and tested in the 4T1 triple-negative model of invasive breast cancer with Poly(I:C) adjuvant. Vaccine immunogenicity was determined by flow cytometric analysis of in vitro and in vivo T-cell responses. Primary tumor growth and lung metastasis was evaluated by histopathology, flow cytometry and colony formation assay. RESULTS We developed a new bioinformatic pipeline to reliably identify CT exclusive genes as immunogenic targets for immunotherapy. We identified CT genes that are exclusively expressed within the testis, lack detectable thymic expression, and are significantly expressed in multiple tumor types. High tumor germness correlated with tumor progression but not with tumor mutation burden, supporting CTAs as appealing targets in low mutation burden tumors. Importantly, tumor germness also correlated with markers of antitumor immunity. Vaccination of 4T1 tumor-bearing mice with Siglece and Lin28a antigens resulted in increased T-cell antitumor immunity and reduced primary tumor growth and lung metastases. CONCLUSION Our results present a novel strategy for the identification of highly immunogenic CTAs for the development of targeted vaccines that induce antitumor immunity and inhibit metastasis.
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Affiliation(s)
- Jason A Carter
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Stony Brook University, Stony Brook, New York, USA
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Bharati Matta
- Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Jenna Battaglia
- Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Carter Somerville
- Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Benjamin D Harris
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Lyell Immunopharma, South San Francisco, CA, USA
| | - Margaret LaPan
- Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Gurinder S Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Regeneron Pharmaceuticals Inc, Tarrytown, NY, USA
| | - Betsy J Barnes
- Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Departments of Pediatrics and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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Hikmet F, Rassy M, Backman M, Méar L, Mattsson JSM, Djureinovic D, Botling J, Brunnström H, Micke P, Lindskog C. Expression of cancer-testis antigens in the immune microenvironment of non-small cell lung cancer. Mol Oncol 2023; 17:2603-2617. [PMID: 37341056 DOI: 10.1002/1878-0261.13474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 06/22/2023] Open
Abstract
The antigenic repertoire of tumors is critical for successful anti-cancer immune response and the efficacy of immunotherapy. Cancer-testis antigens (CTAs) are targets of humoral and cellular immune reactions. We aimed to characterize CTA expression in non-small cell lung cancer (NSCLC) in the context of the immune microenvironment. Of 90 CTAs validated by RNA sequencing, eight CTAs (DPEP3, EZHIP, MAGEA4, MAGEB2, MAGEC2, PAGE1, PRAME, and TKTL1) were selected for immunohistochemical profiling in cancer tissues from 328 NSCLC patients. CTA expression was compared with immune cell densities in the tumor environment and with genomic, transcriptomic, and clinical data. Most NSCLC cases (79%) expressed at least one of the analyzed CTAs, and CTA protein expression correlated generally with RNA expression. CTA profiles were associated with immune profiles: high MAGEA4 expression was related to M2 macrophages (CD163) and regulatory T cells (FOXP3), low MAGEA4 was associated with T cells (CD3), and high EZHIP was associated with plasma cell infiltration (adj. P-value < 0.05). None of the CTAs correlated with clinical outcomes. The current study provides a comprehensive evaluation of CTAs and suggests that their association with immune cells may indicate in situ immunogenic effects. The findings support the rationale to harness CTAs as targets for immunotherapy.
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Affiliation(s)
- Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Marc Rassy
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Loren Méar
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | | | - Dijana Djureinovic
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
- Department of Medicine (Medical Oncology), Yale University School of Medicine, New Haven, CT, USA
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Hans Brunnström
- Division of Pathology, Department of Clinical Sciences Lund, Lund University, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
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9
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Kurkalang S, Roy S, Acharya A, Mazumder P, Mazumder S, Patra S, Ghosh S, Sarkar S, Kundu S, Biswas NK, Ghose S, Majumder PP, Maitra A. Single-cell transcriptomic analysis of gingivo-buccal oral cancer reveals two dominant cellular programs. Cancer Sci 2023; 114:4732-4746. [PMID: 37792582 PMCID: PMC10728019 DOI: 10.1111/cas.15979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023] Open
Abstract
Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) is the most common cancer among men in India, and is associated with poor prognosis and frequent recurrence. Cellular heterogeneity in OSCC-GB was investigated by single-cell RNA sequencing of tumors derived from the oral cavity of 12 OSCC-GB patients, 3 of whom had concomitant presence of a precancerous lesion (oral submucous fibrosis [OSMF]). Unique malignant cell types, features, and phenotypic shifts in the stromal cell population were identified in oral tumors with associated submucous fibrosis. Expression levels of FOS, ATP1A, and DUSP1 provided robust discrimination between tumors with or without the concomitant presence of OSMF. Malignant cell populations shared between tumors with and without OSMF were enriched with the expression of partial epithelial-mesenchymal transition (pEMT) or fetal cell type signatures indicative of two dominant cellular programs in OSCC-GB-pEMT and fetal cellular reprogramming. Malignant cells exhibiting fetal cellular and pEMT programs were enriched with the expression of immune-related pathway genes known to be involved in antitumor immune response. In the tumor microenvironment, higher infiltration of immune cells than the stromal cells was observed. The T cell population was large in tumors and diverse subtypes of T cells with varying levels of infiltration were found. We also detected double-negative PLCG2+ T cells and cells with intermediate M1-M2 macrophage polarization. Our findings shed light on unique aspects of cellular heterogeneity and cell states in OSCC-GB.
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Affiliation(s)
| | - Sumitava Roy
- National Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
| | - Arunima Acharya
- National Institute of Biomedical GenomicsKalyaniIndia
- Regional Centre for BiotechnologyFaridabadIndia
| | - Paramita Mazumder
- Department of Oral PathologyDr. R. Ahmed Dental College and HospitalKolkataIndia
| | | | - Subrata Patra
- National Institute of Biomedical GenomicsKalyaniIndia
| | - Shekhar Ghosh
- National Institute of Biomedical GenomicsKalyaniIndia
| | | | - Sudip Kundu
- National Institute of Biomedical GenomicsKalyaniIndia
| | | | - Sandip Ghose
- Department of Oral PathologyDr. R. Ahmed Dental College and HospitalKolkataIndia
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10
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Ai H, Yang H, Li L, Ma J, Liu K, Li Z. Cancer/testis antigens: promising immunotherapy targets for digestive tract cancers. Front Immunol 2023; 14:1190883. [PMID: 37398650 PMCID: PMC10311965 DOI: 10.3389/fimmu.2023.1190883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023] Open
Abstract
Digestive tract cancers, including esophageal, gastric, and colorectal cancers, are the major cause of death among cancer patients worldwide due to the heterogeneity of cancer cells, which limits the effectiveness of traditional treatment methods. Immunotherapy represents a promising treatment strategy for improving the prognosis of patients with digestive tract cancers. However, the clinical application of this approach is limited by the absence of optimal targets. Cancer/testis antigens are characterized by low or absent expression in normal tissues, but high expression in tumor tissues, making them an attractive target for antitumor immunotherapy. Recent preclinical trials have shown promising results for cancer/testis antigen-targeted immunotherapy in digestive cancer. However, practical problems and difficulties in clinical application remain. This review presents a comprehensive analysis of cancer/testis antigens in digestive tract cancers, covering their expression, function, and potential as an immunotherapy target. Additionally, the current state of cancer/testis antigens in digestive tract cancer immunotherapy is discussed, and we predict that these antigens hold great promise as an avenue for breakthroughs in the treatment of digestive tract cancers.
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Affiliation(s)
- Huihan Ai
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Hang Yang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Liang Li
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Jie Ma
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Department of Molecular and Cellular Biology, China-United States (US) Hormel (Henan) Cancer Institute, Zhengzhou, Henan, China
- Research Center of Basic Medicine, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhi Li
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
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11
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Xia A, Yue Q, Zhu M, Xu J, Liu S, Wu Y, Wang Z, Xu Z, An H, Wang Q, Wang S, Sun B. The cancer-testis lncRNA LINC01977 promotes HCC progression by interacting with RBM39 to prevent Notch2 ubiquitination. Cell Death Discov 2023; 9:169. [PMID: 37198207 DOI: 10.1038/s41420-023-01459-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Cancer-testis genes are involved in the occurrence and development of cancer, but the role of cancer-testis-associated lncRNAs (CT-lncRNAs) in hepatocellular carcinoma (HCC) remains to be explored. Here, we discovered a novel CT-lncRNA, LINC01977, based on the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases. LINC01977 was exclusively expressed in testes and highly expressed in HCC. High LINC01977 levels correlated with poorer overall survival (OS) in individuals with HCC. Functional assays showed that LINC01977 promoted HCC growth and metastasis in vitro and in vivo. Mechanistically, LINC01977 directly bound to RBM39 to promote the further entry of Notch2 into the nucleus, thereby preventing the ubiquitination and degradation of Notch2. Furthermore, the RNA binding protein IGF2BP2, one of the m6A modification readers, enhanced the stability of LINC01977, resulting in its high level in HCC. Therefore, the data suggest that LINC01977 interacts with RBM39 and promotes the progression of HCC by inhibiting Notch2 ubiquitination and degradation, indicating that LINC01977 may be a potential biomarker and therapeutic target for HCC patients.
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Affiliation(s)
- Anliang Xia
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Qi Yue
- Nanjing Drum Tower Hospital, Clinical College of Jiangsu University, Nanjing, China
| | - Mingming Zhu
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jianbo Xu
- Department of Hepatobiliary Surgery, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Siyuan Liu
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yue Wu
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Zhangding Wang
- Department of Gastroenterology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhu Xu
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hongda An
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Qiang Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.
| | - Beicheng Sun
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
- Nanjing Drum Tower Hospital, Clinical College of Jiangsu University, Nanjing, China.
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12
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Grizzi F, Chiriva-Internati M, Miranda E, Zaharie R, Hajjar NA, Zaharie F, Del Arco CD, Fernández-Aceñero MJ, Bresalier RS, Moiş E. Sperm protein antigen 17 and Sperm flagellar 1 cancer testis antigens are expressed in a rare case of ciliated foregut cyst of the common hepatic duct. Pathol Res Pract 2023; 247:154546. [PMID: 37224658 DOI: 10.1016/j.prp.2023.154546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
INTRODUCTION Ciliated foregut cysts (CFCs) are frequently described in liver, pancreas and gallbladder and generally considered benign although one case of squamous cell metaplasia and five cases of squamous cell carcinoma arising from a ciliated hepatic foregut cyst have been reported. Here we explore two cancer-testis antigens (CTAs), Sperm protein antigen 17 (SPA17) and Sperm flagellar 1 (SPEF1) expression in a rare case of CFC of the common hepatic duct MATERIALS AND METHODS: 3 µm-thick CFC sections were immunohistochemically treated with antibodies raised against human SPA17 or SPEF1. In silico Protein-Protein Interaction (PPI) network and differential protein expression were also investigated RESULTS: Immunohistochemistry revealed SPA17 and SPEF1 in the cytoplasm of ciliated epithelium. SPA17, but not SPEF1, was also detected in cilia. The PPI networks demonstrated that other CTAs are significantly predicted functional partners with SPA17 and SPEF1. The differential protein expression demonstrated that SPA17 was higher in breast cancer, cholangiocarcinoma, liver hepatocellular carcinoma, uterine corpus endometrial carcinoma, gastric adenocarcinoma, cervical squamous cell carcinoma, bladder urothelial carcinoma. SPEF1 expression was higher in breast cancer, cholangiocarcinoma, uterine corpus endometrial carcinoma and kidney renal papillary cell carcinoma CONCLUSIONS: Our study suggests that further characterization of SPA17 and SPEF1 in patients with CFCs might provide significant insights to understand the mechanisms underlying their potential to malignant transformation.
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Affiliation(s)
- Fabio Grizzi
- Department of Immunology and Inflammation, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.
| | - Maurizio Chiriva-Internati
- Departments of Gastroenterology, Hepatology & Nutrition, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Roxana Zaharie
- Iuliu Hațieganu University of Medicine and Pharmacy, Regional Institute of Gastroenterology and Hepatology, Cluj-Napoca, Romania
| | - Nadim Al Hajjar
- Iuliu Hațieganu University of Medicine and Pharmacy, Regional Institute of Gastroenterology and Hepatology, Cluj-Napoca, Romania
| | - Florin Zaharie
- Iuliu Hațieganu University of Medicine and Pharmacy, Regional Institute of Gastroenterology and Hepatology, Cluj-Napoca, Romania
| | | | | | - Robert S Bresalier
- Departments of Gastroenterology, Hepatology & Nutrition, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emil Moiş
- Iuliu Hațieganu University of Medicine and Pharmacy, Regional Institute of Gastroenterology and Hepatology, Cluj-Napoca, Romania
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13
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Carter JA, Matta B, Battaglia J, Somerville C, Harris BD, LaPan M, Atwal GS, Barnes BJ. Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539617. [PMID: 37214884 PMCID: PMC10197572 DOI: 10.1101/2023.05.09.539617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Cancer-testis (CT) genes are targets for tumor antigen-specific immunotherapy given that their expression is normally restricted to the immune-privileged testis in healthy individuals with aberrant expression in tumor tissues. While they represent targetable germ-tissue antigens and play important functional roles in tumorigenesis, there is currently no standardized approach for identifying clinically relevant CT genes. Optimized algorithms and validated methods for accurate prediction of reliable CT antigens with high immunogenicity are also lacking. Methods Sequencing data from the Genotype-Tissue Expression (GTEx) and The Genomic Data Commons (GDC) databases was utilized for the development of a bioinformatic pipeline to identify CT exclusive genes. A CT germness score was calculated based on the number of CT genes expressed within a tumor type and their degree of expression. The impact of tumor germness with clinical outcome was evaluated using healthy GTEx and GDC tumor samples. We then used a triple-negative breast cancer mouse model to develop and test an algorithm that predicts epitope immunogenicity based on the identification of germline sequences with strong MHCI and MHCII binding affinities. Germline sequences for CT genes were synthesized as long synthetic peptide vaccines and tested in the 4T1 triple-negative model of invasive breast cancer with Poly(I:C) adjuvant. Vaccine immunogenicity was determined by flow cytometric analysis of in vitro and in vivo T cell responses. Primary tumor growth and lung metastasis was evaluated by histopathology, flow cytometry and colony formation assay. Results We developed a new bioinformatic pipeline to reliably identify CT exclusive genes as immunogenic targets for immunotherapy. We identified CT genes that are exclusively expressed within the testis, lack detectable thymic expression, and are significantly expressed in multiple tumor types. High tumor germness correlated with tumor progression but not with tumor mutation burden, supporting CT antigens as appealing targets in low mutation burden tumors. Importantly, tumor germness also correlated with markers of anti-tumor immunity. Vaccination of 4T1 tumor bearing mice with Siglece and Lin28a antigens resulted in increased T cell anti-tumor immunity and reduced primary tumor growth and lung metastases. Conclusion Our results present a novel strategy for the identification of highly immunogenic CT antigens for the development of targeted vaccines that induce anti-tumor immunity and inhibit metastasis.
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14
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Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
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Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
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15
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Wang Y, Bedford MT. Effectors and effects of arginine methylation. Biochem Soc Trans 2023; 51:725-734. [PMID: 37013969 PMCID: PMC10212539 DOI: 10.1042/bst20221147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 04/05/2023]
Abstract
Arginine methylation is a ubiquitous and relatively stable post-translational modification (PTM) that occurs in three types: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). Methylarginine marks are catalyzed by members of the protein arginine methyltransferases (PRMTs) family of enzymes. Substrates for arginine methylation are found in most cellular compartments, with RNA-binding proteins forming the majority of PRMT targets. Arginine methylation often occurs in intrinsically disordered regions of proteins, which impacts biological processes like protein-protein interactions and phase separation, to modulate gene transcription, mRNA splicing and signal transduction. With regards to protein-protein interactions, the major 'readers' of methylarginine marks are Tudor domain-containing proteins, although additional domain types and unique protein folds have also recently been identified as methylarginine readers. Here, we will assess the current 'state-of-the-art' in the arginine methylation reader field. We will focus on the biological functions of the Tudor domain-containing methylarginine readers and address other domains and complexes that sense methylarginine marks.
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Affiliation(s)
- Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
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16
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Moscona R, Janssen SM, Elchebly M, Papadakis AI, Rubin E, Spatz A. BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells. Pigment Cell Melanoma Res 2023; 36:299-313. [PMID: 37082838 DOI: 10.1111/pcmr.13089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023]
Abstract
Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of regulator of imprinted sites (BORIS), also known as CCCTC binding factor-like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of melanoma cells from an intermediate melanocytic state toward a more mesenchymal-like state. However, the mechanism underlying this transcriptional switch remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in melanoma cells harboring an intermediate melanocytic state. The gene set that gained promoter accessibility, following ectopic BORIS expression, showed enrichment for biological processes associated with melanoma invasion, while promoters of genes associated with proliferation showed reduced accessibility. Integration of ATAC-seq and RNA-seq data demonstrated that increased chromatin accessibility was associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes were associated with repressed activity of tumor suppressors and proliferation factors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of melanoma cells toward a mesenchymal-like genetic signature.
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Affiliation(s)
- Roy Moscona
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sanne Marlijn Janssen
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
| | | | | | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Alan Spatz
- Lady Davis Institute, Montréal, Quebec, Canada
- Department of Pathology, McGill University, Montréal, Quebec, Canada
- Division of Pathology, Department of Laboratory Medicine, McGill University Health Center, Montréal, Quebec, Canada
- Department of Oncology, McGill University, Montréal, Quebec, Canada
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17
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Wood CS, Pennel KA, Leslie H, Legrini A, Cameron AJ, Melissourgou-Syka L, Quinn JA, van Wyk HC, Hay J, Roseweir AK, Nixon C, Roxburgh CS, McMillan DC, Biankin AV, Sansom OJ, Horgan PG, Edwards J, Steele CW, Jamieson NB. Spatially Resolved Transcriptomics Deconvolutes Prognostic Histological Subgroups in Patients with Colorectal Cancer and Synchronous Liver Metastases. Cancer Res 2023; 83:1329-1344. [PMID: 37057593 PMCID: PMC10102851 DOI: 10.1158/0008-5472.can-22-2794] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/11/2022] [Accepted: 02/07/2023] [Indexed: 04/15/2023]
Abstract
Strong immune responses in primary colorectal cancer correspond with better patient survival following surgery compared with tumors with predominantly stromal microenvironments. However, biomarkers to identify patients with colorectal cancer liver metastases (CRLM) with good prognosis following surgery for oligometastatic disease remain elusive. The aim of this study was to determine the practical application of a simple histological assessment of immune cell infiltration and stromal content in predicting outcome following synchronous resection of primary colorectal cancer and CRLM and to interrogate the underlying functional biology that drives disease progression. Samples from patients undergoing synchronous resection of primary colorectal cancer and CRLM were evaluated in detail through histological assessment, panel genomic and bulk transcriptomic assessment, IHC, and GeoMx spatial transcriptomics (ST) analysis. High immune infiltration of metastases was associated with improved cancer-specific survival. Bulk transcriptomic analysis was confounded by stromal content, but ST demonstrated that the invasive edge of the metastases of long-term survivors was characterized by adaptive immune cell populations enriched for type II IFN signaling and MHC-class II antigen presentation. In contrast, patients with poor prognosis demonstrated increased abundance of regulatory T cells and neutrophils with enrichment of Notch and TGFβ signaling pathways at the metastatic tumor center. In summary, histological assessment can stratify outcomes in patients undergoing synchronous resection of CRLM, suggesting that it has potential as a prognostic biomarker. Furthermore, ST analysis has revealed significant intratumoral and interlesional heterogeneity and identified the underlying transcriptomic programs driving each phenotype. SIGNIFICANCE Spatial transcriptomics uncovers heterogeneity between patients, between matched lesions in the same patient, and within individual lesions and identifies drivers of metastatic progression in colorectal cancer with reactive and suppressed immune microenvironments.
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Affiliation(s)
- Colin S. Wood
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Holly Leslie
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Assya Legrini
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Andrew J. Cameron
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Jean A. Quinn
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hester C. van Wyk
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jennifer Hay
- Glasgow Tissue Research Facility, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | | | - Colin Nixon
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Campbell S.D. Roxburgh
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Donald C. McMillan
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Andrew V. Biankin
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Owen J. Sansom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Paul G. Horgan
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Joanne Edwards
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Colin W. Steele
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- CRUK Beatson Institute, Glasgow, United Kingdom
| | - Nigel B. Jamieson
- University Department of Surgery, Glasgow Royal Infirmary, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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18
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Immunotherapy in breast cancer: an overview of current strategies and perspectives. NPJ Breast Cancer 2023; 9:7. [PMID: 36781869 PMCID: PMC9925769 DOI: 10.1038/s41523-023-00508-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/21/2023] [Indexed: 02/15/2023] Open
Abstract
Recent progress in immunobiology has led the way to successful host immunity enhancement against breast cancer. In triple-negative breast cancer, the combination of cancer immunotherapy based on PD-1/PD-L1 immune checkpoint inhibitors with chemotherapy was effective both in advanced and early setting phase 3 clinical trials. These encouraging results lead to the first approvals of immune checkpoint inhibitors in triple-negative breast cancer and thus offer new therapeutic possibilities in aggressive tumors and hard-to-treat populations. Furthermore, several ongoing trials are investigating combining immunotherapies involving immune checkpoint inhibitors with conventional therapies and as well as with other immunotherapeutic strategies such as cancer vaccines, CAR-T cells, bispecific antibodies, and oncolytic viruses in all breast cancer subtypes. This review provides an overview of immunotherapies currently under clinical development and updated key results from clinical trials. Finally, we discuss the challenges to the successful implementation of immune treatment in managing breast cancer and their implications for the design of future clinical trials.
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19
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Epigenetic Perspective of Immunotherapy for Cancers. Cells 2023; 12:cells12030365. [PMID: 36766706 PMCID: PMC9913322 DOI: 10.3390/cells12030365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023] Open
Abstract
Immunotherapy has brought new hope for cancer patients in recent times. However, despite the promising success of immunotherapy, there is still a need to address major challenges including heterogeneity in response among patients, the reoccurrence of the disease, and iRAEs (immune-related adverse effects). The first critical step towards solving these issues is understanding the epigenomic events that play a significant role in the regulation of specific biomolecules in the context of the immune population present in the tumor immune microenvironment (TIME) during various treatments and responses. A prominent advantage of this step is that it would enable researchers to harness the reversibility of epigenetic modifications for their druggability. Therefore, we reviewed the crucial studies in which varying epigenomic events were captured with immuno-oncology set-ups. Finally, we discuss the therapeutic possibilities of their utilization for the betterment of immunotherapy in terms of diagnosis, progression, and cure for cancer patients.
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20
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Leiendecker L, Neumann T, Jung PS, Cronin SM, Steinacker TL, Schleiffer A, Schutzbier M, Mechtler K, Kervarrec T, Laurent E, Bachiri K, Coyaud E, Murali R, Busam KJ, Itzinger-Monshi B, Kirnbauer R, Cerroni L, Calonje E, Rütten A, Stubenrauch F, Griewank KG, Wiesner T, Obenauf AC. Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers. Cancer Discov 2023; 13:70-84. [PMID: 36213965 PMCID: PMC9827110 DOI: 10.1158/2159-8290.cd-22-0489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/24/2022] [Accepted: 10/04/2022] [Indexed: 01/13/2023]
Abstract
The skin is exposed to viral pathogens, but whether they contribute to the oncogenesis of skin cancers has not been systematically explored. Here we investigated 19 skin tumor types by analyzing off-target reads from commonly available next-generation sequencing data for viral pathogens. We identified human papillomavirus 42 (HPV42) in 96% (n = 45/47) of digital papillary adenocarcinoma (DPA), an aggressive cancer occurring on the fingers and toes. We show that HPV42, so far considered a nononcogenic, "low-risk" HPV, recapitulates the molecular hallmarks of oncogenic, "high-risk" HPVs. Using machine learning, we find that HPV-driven transformation elicits a germ cell-like transcriptional program conserved throughout all HPV-driven cancers (DPA, cervical carcinoma, and head and neck cancer). We further show that this germ cell-like transcriptional program, even when reduced to the top two genes (CDKN2A and SYCP2), serves as a fingerprint of oncogenic HPVs with implications for early detection, diagnosis, and therapy of all HPV-driven cancers. SIGNIFICANCE We identify HPV42 as a uniform driver of DPA and add a new member to the short list of tumorigenic viruses in humans. We discover that all oncogenic HPVs evoke a germ cell-like transcriptional program with important implications for detecting, diagnosing, and treating all HPV-driven cancers. See related commentary by Starrett et al., p. 17. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Lukas Leiendecker
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Quantro Therapeutics, Vienna, Austria
| | - Pauline S. Jung
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Shona M. Cronin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas L. Steinacker
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michael Schutzbier
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Thibault Kervarrec
- Department of Pathology, University Hospital Center of Tours, University of Tours, Tours, France
| | - Estelle Laurent
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Kamel Bachiri
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Etienne Coyaud
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J. Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Reinhard Kirnbauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Eduardo Calonje
- Department of Dermatopathology, St John's Institute of Dermatology, St Thomas’ Hospital, London, United Kingdom
| | - Arno Rütten
- Dermatopathology Friedrichshafen, Friedrichshafen, Germany
| | - Frank Stubenrauch
- University Hospital Tuebingen, Institute for Medical Virology and Epidemiology of Viral Diseases, Tuebingen, Germany
| | - Klaus G. Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg, German Cancer Consortium (DKTK), Partner Site, Essen, Germany
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
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21
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Bruggeman JW, Koster J, van Pelt AMM, Speijer D, Hamer G. How germline genes promote malignancy in cancer cells. Bioessays 2023; 45:e2200112. [PMID: 36300921 DOI: 10.1002/bies.202200112] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 02/01/2023]
Abstract
Cancers often express hundreds of genes otherwise specific to germ cells, the germline/cancer (GC) genes. Here, we present and discuss the hypothesis that activation of a "germline program" promotes cancer cell malignancy. We do so by proposing four hallmark processes of the germline: meiosis, epigenetic plasticity, migration, and metabolic plasticity. Together, these hallmarks enable replicative immortality of germ cells as well as cancer cells. Especially meiotic genes are frequently expressed in cancer, implying that genes unique to meiosis may play a role in oncogenesis. Because GC genes are not expressed in healthy somatic tissues, they form an appealing source of specific treatment targets with limited side effects besides infertility. Although it is still unclear why germ cell specific genes are so abundantly expressed in cancer, from our hypothesis it follows that the germline's reproductive program is intrinsic to cancer development.
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Affiliation(s)
- Jan Willem Bruggeman
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Ans M M van Pelt
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Geert Hamer
- Reproductive Biology Laboratory, Center for Reproductive Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development research institute, Amsterdam, The Netherlands
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22
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van Amerongen RA, Tuit S, Wouters AK, van de Meent M, Siekman SL, Meeuwsen MH, Wachsmann TLA, Remst DFG, Hagedoorn RS, van der Steen DM, de Ru AH, Verdegaal EME, van Veelen PA, Falkenburg JHF, Heemskerk MHM. PRAME and CTCFL-reactive TCRs for the treatment of ovarian cancer. Front Immunol 2023; 14:1121973. [PMID: 37026005 PMCID: PMC10070997 DOI: 10.3389/fimmu.2023.1121973] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 04/08/2023] Open
Abstract
Recurrent disease emerges in the majority of patients with ovarian cancer (OVCA). Adoptive T-cell therapies with T-cell receptors (TCRs) targeting tumor-associated antigens (TAAs) are considered promising solutions for less-immunogenic 'cold' ovarian tumors. In order to treat a broader patient population, more TCRs targeting peptides derived from different TAAs binding in various HLA class I molecules are essential. By performing a differential gene expression analysis using mRNA-seq datasets, PRAME, CTCFL and CLDN6 were selected as strictly tumor-specific TAAs, with high expression in ovarian cancer and at least 20-fold lower expression in all healthy tissues of risk. In primary OVCA patient samples and cell lines we confirmed expression and identified naturally expressed TAA-derived peptides in the HLA class I ligandome. Subsequently, high-avidity T-cell clones recognizing these peptides were isolated from the allo-HLA T-cell repertoire of healthy individuals. Three PRAME TCRs and one CTCFL TCR of the most promising T-cell clones were sequenced, and transferred to CD8+ T cells. The PRAME TCR-T cells demonstrated potent and specific antitumor reactivity in vitro and in vivo. The CTCFL TCR-T cells efficiently recognized primary patient-derived OVCA cells, and OVCA cell lines treated with demethylating agent 5-aza-2'-deoxycytidine (DAC). The identified PRAME and CTCFL TCRs are promising candidates for the treatment of patients with ovarian cancer, and are an essential addition to the currently used HLA-A*02:01 restricted PRAME TCRs. Our selection of differentially expressed genes, naturally expressed TAA peptides and potent TCRs can improve and broaden the use of T-cell therapies for patients with ovarian cancer or other PRAME or CTCFL expressing cancers.
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Affiliation(s)
| | - Sander Tuit
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Anne K. Wouters
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Sterre L. Siekman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Miranda H. Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Dennis F. G. Remst
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Els M. E. Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Mirjam H. M. Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
- *Correspondence: Mirjam H. M. Heemskerk,
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23
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Wang D. Targeting the stage-specific embryonic antigen (SSEA)-0 tumor neoantigen. CURRENT TRENDS IN IMMUNOLOGY 2023; 24:1-7. [PMID: 38699667 PMCID: PMC11064955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Recognition of abnormal glycosylation in virtually any cancer type has raised a great interest in the glycan-based tumor biomarkers. Our team explored carbohydrate microarrays as a broad-spectrum immunoassay to probe the immunologically potent tumor glycan targets. This effort has led to the identification of a blood group precursor antigen SSEA-0 as a conserved breast cancer (BCA) marker. Since this immunogenic O-core glycan is normally hidden as a cryptic antigen but becomes overexpressed and surface-exposed by metastatic breast cancer cells (MBCA), its potential as a novel immunological target for precision immunotherapy against tumor metastasis warrants a focused investigation.
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Affiliation(s)
- Denong Wang
- Tumor Glycomics Laboratory, SRI International Biosciences Division, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493, USA
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24
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Noordam L, de Beijer MT, Mancham S, Vogler I, Boor PP, de Ruiter V, Luijten R, IJzermans JN, Sahin U, Bruno MJ, Sprengers D, Buschow SI, Kwekkeboom J. Systemic T-cell and humoral responses against cancer testis antigens in hepatocellular carcinoma patients. Oncoimmunology 2022; 11:2131096. [PMID: 36211805 PMCID: PMC9542711 DOI: 10.1080/2162402x.2022.2131096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related deaths worldwide due to high recurrence rates after curative treatment and being frequently diagnosed at an advanced stage. Immune-checkpoint inhibition (ICPI) has yielded impressive clinical successes in a variety of solid cancers, however results in treatment of HCC have been modest. Vaccination could be a promising treatment to synergize with ICPI and enhance response rates. Cancer testis antigens (CTAs) were recently discovered to be widely expressed in HCC and expression in macroscopically tumor-free tissues correlated with recurrence, implying the presence of micro-satellites. To determine whether CTAs are immunogenic in HCC patients, we analyzed systemic T-cell and humoral responses against seven CTAs in 38 HCC patients using a multitude of techniques; flowcytometry, ELISA and whole antigen and peptide stimulation assays. CTA-specific T-cells were detected in all (25/25) analyzed patients, of which most had a memory phenotype but did not exhibit unequivocal signs of chronic stimulation or recent antigen encounter. Proliferative CD4+ and CD8+ T-cell responses against these CTAs were found in 14/16 analyzed HCC patients. CTA-peptide stimulation-induced granzyme B, IL2, and TNFa in 8/8 analyzed patients, including two MAGEA1 peptides included based on in silico prediction. Finally, IgG responses were observed in 13/32 patients, albeit with low titers. The presence of CD4+ and CD8+ T-cells and IgG responses shows the immunogenicity of these CTAs in HCC-patients. We hypothesize that vaccines based on these tumor-specific antigens may boost preexisting CTA-specific immunity and could enhance therapeutic efficacy of ICPI in advanced HCC.
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Affiliation(s)
- Lisanne Noordam
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Monique T.A. de Beijer
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Shanta Mancham
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | | | - Patrick P.C. Boor
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Valeska de Ruiter
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Robbie Luijten
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Jan N.M. IJzermans
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | | | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Dave Sprengers
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Sonja I. Buschow
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Jaap Kwekkeboom
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
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25
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Wang Y, Huang P, Wang BG, Murdock T, Cope L, Hsu FC, Wang TL, Shih IM. Spatial Transcriptomic Analysis of Ovarian Cancer Precursors Reveals Reactivation of IGFBP2 during Pathogenesis. Cancer Res 2022; 82:4528-4541. [PMID: 36206311 PMCID: PMC9808976 DOI: 10.1158/0008-5472.can-22-1620] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/15/2022] [Accepted: 10/03/2022] [Indexed: 01/24/2023]
Abstract
Elucidating the earliest pathogenic steps in cancer development is fundamental to improving its early detection and prevention. Ovarian high-grade serous carcinoma (HGSC), a highly aggressive cancer, mostly originates from the fallopian tube epithelium through a precursor stage, serous tubal intraepithelial carcinoma (STIC). In this study, we performed spatial transcriptomic analysis to compare STICs, carcinoma, and their matched normal fallopian tube epithelium. Several differentially expressed genes in STICs and carcinomas were involved in cancer metabolism and detected in a larger independent transcriptomic dataset of ovarian HGSCs. Among these, insulin-like growth factor binding protein-2 (IGFBP2) was found to undergo DNA hypomethylation and to be increased at the protein level in STICs. Pyrosequencing revealed an association of IGFBP2 expression with the methylation state of its proximal enhancer, and 5-azacytidine treatment increased IGFBP2 expression. In postmenopausal fallopian tubes, where most STICs are detected, IGFBP2 immunoreactivity was detected in all 38 proliferatively active STICs but was undetectable in morphologically normal tubal epithelia, including those with TP53 mutations. In premenopausal fallopian tubes, IGFBP2 expression was limited to the secretory epithelium at the proliferative phase, and estradiol treatment increased IGFBP2 expression levels. IGFBP2 knockdown suppressed the growth of IGFBP2-expressing tubal epithelial cells via inactivation of the AKT pathway. Taken together, demethylation of the proximal enhancer of IGFBP2 drives tumor development by maintaining the increased IGFBP2 required for proliferation in an otherwise estrogen-deprived, proliferation-quiescent, and postmenopausal tubal microenvironment. SIGNIFICANCE Molecular studies of the earliest precursor lesions of ovarian cancer reveal a role of IGFBP2 in propelling tumor initiation, providing new insights into ovarian cancer development.
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Affiliation(s)
- Yeh Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peng Huang
- Biostatistics Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Brant G. Wang
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia
| | - Tricia Murdock
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leslie Cope
- Biostatistics Division, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fang-Chi Hsu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Gynecology and Obstetrics and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Gynecology and Obstetrics and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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26
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Kilanowska A, Ziółkowska A, Stasiak P, Gibas-Dorna M. cAMP-Dependent Signaling and Ovarian Cancer. Cells 2022; 11:cells11233835. [PMID: 36497095 PMCID: PMC9738761 DOI: 10.3390/cells11233835] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
cAMP-dependent pathway is one of the most significant signaling cascades in healthy and neoplastic ovarian cells. Working through its major effector proteins-PKA and EPAC-it regulates gene expression and many cellular functions. PKA promotes the phosphorylation of cAMP response element-binding protein (CREB) which mediates gene transcription, cell migration, mitochondrial homeostasis, cell proliferation, and death. EPAC, on the other hand, is involved in cell adhesion, binding, differentiation, and interaction between cell junctions. Ovarian cancer growth and metabolism largely depend on changes in the signal processing of the cAMP-PKA-CREB axis, often associated with neoplastic transformation, metastasis, proliferation, and inhibition of apoptosis. In addition, the intracellular level of cAMP also determines the course of other pathways including AKT, ERK, MAPK, and mTOR, that are hypo- or hyperactivated among patients with ovarian neoplasm. With this review, we summarize the current findings on cAMP signaling in the ovary and its association with carcinogenesis, multiplication, metastasis, and survival of cancer cells. Additionally, we indicate that targeting particular stages of cAMP-dependent processes might provide promising therapeutic opportunities for the effective management of patients with ovarian cancer.
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Affiliation(s)
- Agnieszka Kilanowska
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, 65-046 Zielona Gora, Poland
- Correspondence: ; Tel.: +48-683-283-148
| | - Agnieszka Ziółkowska
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, 65-046 Zielona Gora, Poland
| | - Piotr Stasiak
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, 65-046 Zielona Gora, Poland
| | - Magdalena Gibas-Dorna
- Department of Anatomy and Histology, Collegium Medicum, University of Zielona Gora, 65-046 Zielona Gora, Poland
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27
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Gao H, Cai B, Lu Z, Wang G, Gao Y, Miao Y, Jiang K, Zhang K. Cancer‐testis gene
STK31
is regulated by methylation and promotes the development of pancreatic cancer. Cancer Med 2022; 12:7273-7282. [PMID: 36424885 PMCID: PMC10067059 DOI: 10.1002/cam4.5472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/22/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUD Pancreatic cancer (PC) is a highly invasive malignancy with extremely poor prognosis. STK31 has been identified as a cancer-testis (CT) gene, but its function in PC has not been elucidated well. METHODS The effect of STK31 on cell proliferation, migration and invasion was investigated by in vitro and in vivo experiments and total RNA sequencing and targeted bisulfite sequencing was applied to explore the potential regulatory mechanisms of STK31 in PC. RESULTS By analysis of tissue samples and the clinicopathologic features, we found that STK31 was reactivated in PC and associated with poor prognosis. In addition, the vitro and vivo studies indicated that STK31 could promote PC progression by facilitating cell proliferation, migration and invasion, and the indication. Targeted Bisulfite Sequencing showed that STK31 was regulated by methylation. Furthermore, the results of total RNA sequencing suggested that STK31 was closely related to signal transduction, metabolism, and the immune system. CONCLUSIONS This study demonstrates that STK31, as a CT gene, can promote the development of PC and is regulated by methylation. STK31 could be considered as a potential therapeutic target for PC.
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Affiliation(s)
- Hao Gao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Baobao Cai
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Zipeng Lu
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Guangfu Wang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Yong Gao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Yi Miao
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Kuirong Jiang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
| | - Kai Zhang
- Pancreas Center the First Affiliated Hospital of Nanjing Medical University Nanjing China
- Pancreas Institution of Nanjing Medical University Nanjing China
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28
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Wang C, Dai J, Qin N, Fan J, Ma H, Chen C, An M, Zhang J, Yan C, Gu Y, Xie Y, He Y, Jiang Y, Zhu M, Song C, Jiang T, Liu J, Zhou J, Wang N, Hua T, Liang S, Wang L, Xu J, Yin R, Chen L, Xu L, Jin G, Lin D, Hu Z, Shen H. Analyses of rare predisposing variants of lung cancer in 6,004 whole genomes in Chinese. Cancer Cell 2022; 40:1223-1239.e6. [PMID: 36113475 DOI: 10.1016/j.ccell.2022.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
We present the largest whole-genome sequencing (WGS) study of non-small cell lung cancer (NSCLC) to date among 6,004 individuals of Chinese ancestry, coupled with 23,049 individuals genotyped by SNP array. We construct a high-quality haplotype reference panel for imputation and identify 20 common and low-frequency loci (minor allele frequency [MAF] ≥ 0.5%), including five loci that have never been reported before. For rare loss-of-function (LoF) variants (MAF < 0.5%), we identify BRCA2 and 18 other cancer predisposition genes that affect 5.29% of individuals with NSCLC, and 98.91% (181 of 183) of LoF variants have not been linked previously to NSCLC risk. Promoter variants of BRCA2 also have a substantial effect on NSCLC risk, and their prevalence is comparable with BRCA2 LoF variants. The associations are validated in an independent case-control study including 4,410 individuals and a prospective cohort study including 23,826 individuals. Our findings not only provide a high-quality reference panel for future array-based association studies but depict the whole picture of rare pathogenic variants for NSCLC.
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Affiliation(s)
- Cheng Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Juncheng Dai
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Na Qin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jingyi Fan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Hongxia Ma
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Congcong Chen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Mingxing An
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jing Zhang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Caiwang Yan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yayun Gu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuanlin He
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yue Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Meng Zhu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Ci Song
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tao Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jia Liu
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jun Zhou
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Nanxi Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tingting Hua
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Shuang Liang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Lu Wang
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jing Xu
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Liang Chen
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Guangfu Jin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhibin Hu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China.
| | - Hongbing Shen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China.
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Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line. Proc Natl Acad Sci U S A 2022; 119:e2204071119. [PMID: 36179046 PMCID: PMC9549395 DOI: 10.1073/pnas.2204071119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
This work originated from mining of cancer genome data and proceeded to analyze the effects of ectopic expression of meiotic cohesins in mitotic cells in culture. In the process, apart from conclusively answering the question on mechanisms for RAD21L toxicity and its underrepresentation in tumor transcriptomes, we found an association of meiotic cohesin binding with BORIS/CTCFL sites in the normal testis. We also elucidated the patterns and outcomes of meiotic cohesin binding to chromosomes in model cell lines. Furthermore, we uncovered that RAD21L-based meiotic cohesin possesses a self-contained chromosome restructuring activity able to trigger sustainable but imperfect mitotic arrest leading to chromosomal instability. The discovered epigenomic and genetic mechanisms can be relevant to chromosome instability in cancer. Many tumors express meiotic genes that could potentially drive somatic chromosome instability. While germline cohesin subunits SMC1B, STAG3, and REC8 are widely expressed in many cancers, messenger RNA and protein for RAD21L subunit are expressed at very low levels. To elucidate the potential of meiotic cohesins to contribute to genome instability, their expression was investigated in human cell lines, predominately in DLD-1. While the induction of the REC8 complex resulted in a mild mitotic phenotype, the expression of the RAD21L complex produced an arrested but viable cell pool, thus providing a source of DNA damage, mitotic chromosome missegregation, sporadic polyteny, and altered gene expression. We also found that genomic binding profiles of ectopically expressed meiotic cohesin complexes were reminiscent of their corresponding specific binding patterns in testis. Furthermore, meiotic cohesins were found to localize to the same sites as BORIS/CTCFL, rather than CTCF sites normally associated with the somatic cohesin complex. These findings highlight the existence of a germline epigenomic memory that is conserved in cells that normally do not express meiotic genes. Our results reveal a mechanism of action by unduly expressed meiotic cohesins that potentially links them to aneuploidy and chromosomal mutations in affected cells.
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Wang Y, Liu L, Tan C, Meng G, Meng L, Nie H, Du J, Lu GX, Lin G, He WB, Tan YQ. Novel MEIOB variants cause primary ovarian insufficiency and non-obstructive azoospermia. Front Genet 2022; 13:936264. [PMID: 35991565 PMCID: PMC9388730 DOI: 10.3389/fgene.2022.936264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Infertility is a global health concern. MEIOB has been found to be associated with premature ovarian insufficiency (POI) and non-obstructive azoospermia (NOA), but its variants have not been reported in Chinese patients. The aim of this study was to identify the genetic aetiology of POI or NOA in three Han Chinese families.Methods: Whole-exome sequencing (WES) was used to identify candidate pathogenic variants in three consanguineous Chinese infertile families with POI or NOA. Sanger sequencing was performed to validate these variants in the proband of family I and her affected family members. In vitro functional analyses were performed to confirm the effects of these variants.Results: Two novel homozygous frameshift variants (c.258_259del and c.1072_1073del) and one novel homozygous nonsense variant (c.814C > T) in the MEIOB gene were identified in three consanguineous Han Chinese families. In vitro functional analyses revealed that these variants produced truncated proteins and affected their function.Conclusion: We identified three novel MEIOB loss-of-function variants in local Chinese patients for the first time and confirmed their pathogenicity using in vitro functional analyses. These results extend the mutation spectrum of the MEIOB gene and have important significance for genetic counselling in these families.
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Affiliation(s)
- Yurong Wang
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, China
| | - Ling Liu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Guiquan Meng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Lanlan Meng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Hongchuan Nie
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Guang-Xiu Lu
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
| | - Wen-Bin He
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
- *Correspondence: Wen-Bin He, ; Yue-Qiu Tan,
| | - Yue-Qiu Tan
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha, China
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- National Engineering and Research Center of Human Stem Cells, Changsha, China
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Changsha, China
- *Correspondence: Wen-Bin He, ; Yue-Qiu Tan,
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31
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Peng LJ, Zhou YB, Geng M, Bourova-Flin E, Chuffart F, Zhang WN, Wang T, Gao MQ, Xi MP, Cheng ZY, Zhang JJ, Liu YF, Chen B, Khochbin S, Wang J, Rousseaux S, Mi JQ. Ectopic expression of a combination of 5 genes detects high risk forms of T-cell acute lymphoblastic leukemia. BMC Genomics 2022; 23:467. [PMID: 35751016 PMCID: PMC9233359 DOI: 10.1186/s12864-022-08688-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND T cell acute lymphoblastic leukemia (T-ALL) defines a group of hematological malignancies with heterogeneous aggressiveness and highly variable outcome, making therapeutic decisions a challenging task. We tried to discover new predictive model for T-ALL before treatment by using a specific pipeline designed to discover aberrantly active gene. RESULTS The expression of 18 genes was significantly associated with shorter survival, including ACTRT2, GOT1L1, SPATA45, TOPAZ1 and ZPBP (5-GEC), which were used as a basis to design a prognostic classifier for T-ALL patients. The molecular characterization of the 5-GEC positive T-ALL unveiled specific characteristics inherent to the most aggressive T leukemic cells, including a drastic shut-down of genes located on the mitochondrial genome and an upregulation of histone genes, the latter characterizing high risk forms in adult patients. These cases fail to respond to the induction treatment, since 5-GEC either predicted positive minimal residual disease (MRD) or a short-term relapse in MRD negative patients. CONCLUSION Overall, our investigations led to the discovery of a homogenous group of leukemic cells with profound alterations of their biology. It also resulted in an accurate predictive tool that could significantly improve the management of T-ALL patients.
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Affiliation(s)
- Li-Jun Peng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue-Bo Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mei Geng
- Department of Oncology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ekaterina Bourova-Flin
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,UMR 5309, CNRSINSERM U1209Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Florent Chuffart
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,UMR 5309, CNRSINSERM U1209Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France
| | - Wei-Na Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng-Qing Gao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng-Ping Xi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Jiao-Jiao Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan-Fang Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saadi Khochbin
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,UMR 5309, CNRSINSERM U1209Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France.
| | - Jin Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Sophie Rousseaux
- Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,UMR 5309, CNRSINSERM U1209Université Grenoble-Alpes/Institute for Advanced Biosciences, La Tronche, France.
| | - Jian-Qing Mi
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Laboratory of Molecular Pathology, Pôle de Recherches Sino-Français en Science du Vivant Et Génomique, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Yang P, Qiao Y, Meng M, Zhou Q. Cancer/Testis Antigens as Biomarker and Target for the Diagnosis, Prognosis, and Therapy of Lung Cancer. Front Oncol 2022; 12:864159. [PMID: 35574342 PMCID: PMC9092596 DOI: 10.3389/fonc.2022.864159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/17/2022] [Indexed: 11/15/2022] Open
Abstract
Lung cancer is the leading type of malignant tumour among cancer-caused death worldwide, and the 5-year survival rate of lung cancer patients is only 18%. Various oncogenes are abnormally overexpressed in lung cancer, including cancer/testis antigens (CTAs), which are restrictively expressed in the male testis but are hardly expressed in other normal tissues, if at all. CTAs are aberrantly overexpressed in various types of cancer, with more than 60 CTAs abnormally overexpressed in lung cancer. Overexpression of oncogenic CTAs drives the initiation, metastasis and progression of lung cancer, and is closely associated with poor prognosis in cancer patients. Several CTAs, such as XAGE, SPAG9 and AKAP4, have been considered as biomarkers for the diagnosis and prognostic prediction of lung cancer. More interestingly, due to the high immunogenicity and specificity of CTAs in cancer, several CTAs, including CT45, BCAP31 and ACTL8, have been targeted for developing novel therapeutics against cancer. CTA-based vaccines, chimeric antigen receptor-modified T cells (CAR-T) and small molecules have been used in lung cancer treatment in pre-clinical and early clinical trials, with encouraging results being obtained. However, there are still many hurdles to be overcome before these therapeutics can be routinely used in clinical lung cancer therapy. This review summarises the recent rapid progress in oncogenic CTAs, focusing on CTAs as biomarkers for lung cancer diagnosis and prognostic prediction, and as targets for novel anti-cancer drug discovery and lung cancer therapy. We also identify challenges and opportunities in CTA-based cancer diagnosis and treatment. Finally, we provide perspectives on the mechanisms of oncogenic CTAs in lung cancer development, and we also suggest CTAs as a new platform for lung cancer diagnosis, prognostic prediction, and novel anti-cancer drug discovery.
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Affiliation(s)
- Ping Yang
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, China
| | - Yingnan Qiao
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China
| | - Mei Meng
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China
| | - Quansheng Zhou
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, Soochow University, Suzhou, China.,State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,2011 Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.,National Clinical Research Center for Hematologic Diseases, The Affiliated Hospital of Soochow University, Suzhou, China
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33
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Khazan-Kost S, Cafri G, Melamed Kadosh D, Mooshayef N, Chatterji S, Dominissini D, Manor S, Zisser B, Broday L, Talalai E, Shemer A, Zadok O, Ofek E, Onn A, Admon A, Peled M. Soluble HLA peptidome of pleural effusions is a valuable source for tumor antigens. J Immunother Cancer 2022; 10:jitc-2021-003733. [PMID: 35580925 PMCID: PMC9114951 DOI: 10.1136/jitc-2021-003733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background Soluble human leucocyte antigen (sHLA) molecules, released into the plasma, carry their original peptide cargo and provide insight into the protein synthesis and degradation schemes of their source cells and tissues. Other body fluids, such as pleural effusions, may also contain sHLA-peptide complexes, and can potentially serve as a source of tumor antigens since these fluids are drained from the tumor microenvironment. We explored this possibility by developing a methodology for purifying and analyzing large pleural effusion sHLA class I peptidomes of patients with malignancies or benign diseases. Methods Cleared pleural fluids, cell pellets present in the pleural effusions, and the primary tumor cells cultured from cancer patients’ effusions, were used for immunoaffinity purification of the HLA molecules. The recovered HLA peptides were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and the resulting LC-MS/MS data were analyzed with the MaxQuant software tool. Selected tumor antigen peptides were tested for their immunogenicity potential with donor peripheral blood mononuclear cells (PBMCs) in an in vitro assay. Results Mass spectrometry analysis of the pleural effusions revealed 39,669 peptides attributable to 11,305 source proteins. The majority of peptides identified from the pleural effusions were defined as HLA ligands that fit the patients’ HLA consensus sequence motifs. The membranal and soluble HLA peptidomes of each individual patient correlated to each other. Additionally, soluble HLA peptidomes from the same patient, obtained at different visits to the clinic, were highly similar. Compared with benign effusions, the soluble HLA peptidomes of malignant pleural effusions were larger and included HLA peptides derived from known tumor-associated antigens, including cancer/testis antigens, lung-related proteins, and vascular endothelial growth factor pathway proteins. Selected tumor-associated antigens that were identified by the immunopeptidomics were able to successfully prime CD8+ T cells. Conclusions Pleural effusions contain sHLA-peptide complexes, and the pleural effusion HLA peptidome of patients with malignant tumors can serve as a rich source of biomarkers for tumor diagnosis and potential candidates for personalized immunotherapy.
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Affiliation(s)
- Sofia Khazan-Kost
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Gal Cafri
- Chaim Sheba Medical Center, Ramat Gan, Israel
| | | | - Navit Mooshayef
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Sumit Chatterji
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dan Dominissini
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Manor
- Ezer Mizion Bone Marrow Donor Registry, Petah Tikva, Israel
| | - Bracha Zisser
- Ezer Mizion Bone Marrow Donor Registry, Petah Tikva, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Efrosiniia Talalai
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anat Shemer
- Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Oranit Zadok
- Institute of Oncology, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Efrat Ofek
- Pathology Department, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Amir Onn
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arie Admon
- Faculty of Biology, Technion Israel Institute of Technology, Haifa, Israel
| | - Michael Peled
- Institute of Pulmonary Medicine, Chaim Sheba Medical Center, Ramat Gan, Israel .,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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34
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Lingg L, Rottenberg S, Francica P. Meiotic Genes and DNA Double Strand Break Repair in Cancer. Front Genet 2022; 13:831620. [PMID: 35251135 PMCID: PMC8895043 DOI: 10.3389/fgene.2022.831620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022] Open
Abstract
Tumor cells show widespread genetic alterations that change the expression of genes driving tumor progression, including genes that maintain genomic integrity. In recent years, it has become clear that tumors frequently reactivate genes whose expression is typically restricted to germ cells. As germ cells have specialized pathways to facilitate the exchange of genetic information between homologous chromosomes, their aberrant regulation influences how cancer cells repair DNA double strand breaks (DSB). This drives genomic instability and affects the response of tumor cells to anticancer therapies. Since meiotic genes are usually transcriptionally repressed in somatic cells of healthy tissues, targeting aberrantly expressed meiotic genes may provide a unique opportunity to specifically kill cancer cells whilst sparing the non-transformed somatic cells. In this review, we highlight meiotic genes that have been reported to affect DSB repair in cancers derived from somatic cells. A better understanding of their mechanistic role in the context of homology-directed DNA repair in somatic cancers may provide useful insights to find novel vulnerabilities that can be targeted.
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Affiliation(s)
- Lea Lingg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
- *Correspondence: Sven Rottenberg, ; Paola Francica,
| | - Paola Francica
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Cancer Therapy Resistance Cluster, Department for BioMedical Research, University of Bern, Bern, Switzerland
- *Correspondence: Sven Rottenberg, ; Paola Francica,
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The cancer-testis lncRNA lnc-CTHCC promotes hepatocellular carcinogenesis by binding hnRNP K and activating YAP1 transcription. NATURE CANCER 2022; 3:203-218. [PMID: 35122073 DOI: 10.1038/s43018-021-00315-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
Cancer-testis (CT) genes participate in the initiation and progression of cancer, but the role of CT-associated long non-coding RNAs (CT-lncRNAs) in hepatocellular carcinoma (HCC) is still elusive. Here, we discovered a conserved CT-lncRNA, named lnc-CTHCC, which was highly expressed in the testes and HCC. A lnc-CTHCC-knockout (KO) mouse model further confirmed that the global loss of lnc-CTHCC inhibited the occurrence and development of HCC. In vitro and in vivo assays also showed that lnc-CTHCC promoted HCC growth and metastasis. Mechanistically, lnc-CTHCC bound to heterogeneous nuclear ribonucleoprotein K (hnRNP K), which was recruited to the YAP1 promoter for its activation. Additionally, the N6-methyladenosine (m6A) modification was mediated by N6-adenosine-methyltransferase 70-kDa subunit (METTL3) and recognized by insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)/IGF2BP3, which maintained lnc-CTHCC stability and increased its expression in HCC. Together, our results show that lnc-CTHCC directly binds to hnRNP K and promotes hepatocellular carcinogenesis and progression by activating YAP1 transcription, suggesting that lnc-CTHCC is a potential biomarker and therapeutic target of HCC.
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36
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Meng Y, Du M, Gu D, Li C, Li S, Zhang Q, Ben S, Zhu Q, Xin J, Zhang Z, Hu Z, Shen H, Jiang K, Wang M. Genome-wide association analyses identify CATSPERE as a mediator of colorectal cancer susceptibility and progression. Cancer Res 2022; 82:986-997. [DOI: 10.1158/0008-5472.can-21-2948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/12/2021] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
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37
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Jumaa MG, Ramadhan MAK. Cancer testis antigen XAGE-1 is a promising marker for the diagnosis and treatment of ovarian cancer. J Med Life 2022; 14:710-715. [PMID: 35027975 PMCID: PMC8742904 DOI: 10.25122/jml-2021-0304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Cancer testis antigens have been discovered in various cancers, and several studies have suggested that since they exhibit such distinct patterns of expression, these antigens might be attractive targets for cancer detection and immunotherapy. Our work attempted to clarify the function played by cancer-testis antigens in ovarian cancers, notably in the XAGE1 gene. The investigation was conducted on 74 tissue samples from newly diagnosed patients with ovarian cancer. The control group included twenty-eight benign ovarian tumors. The expression of XAGE1 mRNA was assessed using RT-PCR. Compared to benign tumors, cancer samples exhibited higher levels of XAGE1 gene expression, which was statistically significant (P0.01). There were no statistically significant differences between menopausal status and family history. Gene expression was substantially connected with age groups as the higher level of gene expression in patients 50-74 years of age (P 0.01) was seen. Mucinous tumors exhibited significant correlations (P0.01) across histopathological tumor types. In correlation with tumor stages, stage III was substantially linked compared to stage I (P0.01). In conclusion, we referred to the potential to use XAGE1 to discriminate malignant ovarian tumors as a diagnostic biomarker. The connection of high XAGE 1 level with advanced ovarian cancer stages has also been established, supporting XAGE 1's proposed role in poor prognosis. Finally, finding the specific involvement of this gene in ovarian cancer and other kinds of malignancies may require further investigations.
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Affiliation(s)
- Maysaa Ghazi Jumaa
- Department of Microbiology, College of Medicine, University of Maisan, Maisan, Iraq
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38
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Cho JW, Shim HS, Lee CY, Park SY, Hong MH, Lee I, Kim HR. The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer. Exp Mol Med 2022; 54:12-22. [PMID: 34987166 PMCID: PMC8813945 DOI: 10.1038/s12276-021-00718-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 09/23/2021] [Accepted: 10/29/2021] [Indexed: 01/01/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a subtype of non-small cell lung cancer (NSCLC). LUSC occurs at the bronchi, shows a squamous appearance, and often occurs in smokers. To determine the epigenetic regulatory mechanisms of tumorigenesis, we performed a genome-wide analysis of DNA methylation in tumor and adjacent normal tissues from LUSC patients. With the Infinium Methylation EPIC Array, > 850,000 CpG sites, including ~350,000 CpG sites for enhancer regions, were profiled, and the differentially methylated regions (DMRs) overlapping promoters (pDMRs) and enhancers (eDMRs) between tumor and normal tissues were identified. Dimension reduction based on DMR profiles revealed that eDMRs alone and not pDMRs alone can differentiate tumors from normal tissues with the equivalent performance of total DMRs. We observed a stronger negative correlation of LUSC-specific gene expression with methylation for enhancers than promoters. Target genes of eDMRs rather than pDMRs were found to be enriched for tumor-associated genes and pathways. Furthermore, DMR methylation associated with immune infiltration was more frequently observed among enhancers than promoters. Our results suggest that methylation of enhancer regions rather than promoters play more important roles in epigenetic regulation of tumorigenesis and immune infiltration in LUSC.
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Affiliation(s)
- Jae-Won Cho
- grid.15444.300000 0004 0470 5454Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722 Republic of Korea
| | - Hyo Sup Shim
- grid.15444.300000 0004 0470 5454Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Chang Young Lee
- grid.15444.300000 0004 0470 5454Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Seong Yong Park
- grid.15444.300000 0004 0470 5454Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Min Hee Hong
- grid.15444.300000 0004 0470 5454Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, 03722 Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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The Cancer Surfaceome Atlas integrates genomic, functional and drug response data to identify actionable targets. NATURE CANCER 2021; 2:1406-1422. [PMID: 35121907 PMCID: PMC9940627 DOI: 10.1038/s43018-021-00282-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
Cell-surface proteins (SPs) are a rich source of immune and targeted therapies. By systematically integrating single-cell and bulk genomics, functional studies and target actionability, in the present study we comprehensively identify and annotate genes encoding SPs (GESPs) pan-cancer. We characterize GESP expression patterns, recurrent genomic alterations, essentiality, receptor-ligand interactions and therapeutic potential. We also find that mRNA expression of GESPs is cancer-type specific and positively correlates with protein expression, and that certain GESP subgroups function as common or specific essential genes for tumor cell growth. We also predict receptor-ligand interactions substantially deregulated in cancer and, using systems biology approaches, we identify cancer-specific GESPs with therapeutic potential. We have made this resource available through the Cancer Surfaceome Atlas ( http://fcgportal.org/TCSA ) within the Functional Cancer Genome data portal.
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Bi-allelic variants in human WDR63 cause male infertility via abnormal inner dynein arms assembly. Cell Discov 2021; 7:110. [PMID: 34782613 PMCID: PMC8593051 DOI: 10.1038/s41421-021-00327-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
Inner dynein arm (IDA), composed of a series of protein complex, is necessary to cilia and flagella bend formation and beating. Previous studies indicated that defects of IDA protein complex result in multiple morphological abnormalities of the sperm flagellum (MMAF) and male infertility. However, the genetic causes and molecular mechanisms in the IDAs need further exploration. Here we identified two loss-of-function variants of WDR63 in both MMAF and non-obstructive azoospermia (NOA) affected cohorts. WDR63 encodes an IDA-associated protein that is dominantly expressed in testis. We next generated Wdr63-knockout (Wdr63-KO) mice through the CRISPR-Cas9 technology. Remarkably, Wdr63-KO induced decreased sperm number, abnormal flagellar morphology and male infertility. In addition, transmission electron microscopy assay showed severely disorganized "9 + 2" axoneme and absent inner dynein arms in the spermatozoa from Wdr63-KO male mice. Mechanistically, we found that WDR63 interacted with WDR78 mainly via WD40-repeat domain and is necessary for IDA assembly. Furthermore, WDR63-associated male infertility in human and mice could be overcome by intracytoplasmic sperm injection (ICSI) treatment. In conclusion, the present study demonstrates that bi-allelic variants of WDR63 cause male infertility via abnormal inner dynein arms assembly and flagella formation and can be used as a genetic diagnostic indicator for infertility males.
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41
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Schreiner P, Velasquez MP, Gottschalk S, Zhang J, Fan Y. Unifying heterogeneous expression data to predict targets for CAR-T cell therapy. Oncoimmunology 2021; 10:2000109. [PMID: 34858726 PMCID: PMC8632331 DOI: 10.1080/2162402x.2021.2000109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 10/29/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy combines antigen-specific properties of monoclonal antibodies with the lytic capacity of T cells. An effective and safe CAR-T cell therapy strategy relies on identifying an antigen that has high expression and is tumor specific. This strategy has been successfully used to treat patients with CD19+ B-cell acute lymphoblastic leukemia (B-ALL). Finding a suitable target antigen for other cancers such as acute myeloid leukemia (AML) has proven challenging, as the majority of currently targeted AML antigens are also expressed on hematopoietic progenitor cells (HPCs) or mature myeloid cells. Herein, we developed a computational method to perform a data transformation to enable the comparison of publicly available gene expression data across different datasets or assay platforms. The resulting transformed expression values (TEVs) were used in our antigen prediction algorithm to assess suitable tumor-associated antigens (TAAs) that could be targeted with CAR-T cells. We validated this method by identifying B-ALL antigens with known clinical effectiveness, such as CD19 and CD22. Our algorithm predicted TAAs being currently explored preclinically and in clinical CAR-T AML therapy trials, as well as novel TAAs in pediatric megakaryoblastic AML. Thus, this analytical approach presents a promising new strategy to mine diverse datasets for identifying TAAs suitable for immunotherapy.
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Affiliation(s)
- Patrick Schreiner
- The Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mireya Paulina Velasquez
- Department of Bone Marrow Transplantation and Cell Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cell Therapy, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yiping Fan
- The Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
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42
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Wu SC, Münger K. Role and Clinical Utility of Cancer/Testis Antigens in Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13225690. [PMID: 34830845 PMCID: PMC8616139 DOI: 10.3390/cancers13225690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer/testis (CT) antigens exhibit selective expression predominantly in immunoprivileged tissues in non-pathological contexts but are aberrantly expressed in diverse cancers. Due to their expression pattern, they have historically been attractive targets for immunotherapies. A growing number of studies implicate CT antigens in almost all hallmarks of cancer, suggesting that they may act as cancer drivers. CT antigens are expressed in head and neck squamous cell carcinomas. However, their role in the pathogenesis of these cancers remains poorly studied. Given that CT antigens hold intriguing potential as therapeutic targets and as biomarkers for prognosis and that they can provide novel insights into oncogenic mechanisms, their further study in the context of head and squamous cell carcinoma is warranted.
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Affiliation(s)
- Sharon Changshan Wu
- Molecular Microbiology Program, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
- Correspondence:
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43
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Hu H, Khodadadi-Jamayran A, Dolgalev I, Cho H, Badri S, Chiriboga LA, Zeck B, Lopez De Rodas Gregorio M, Dowling CM, Labbe K, Deng J, Chen T, Zhang H, Zappile P, Chen Z, Ueberheide B, Karatza A, Han H, Ranieri M, Tang S, Jour G, Osman I, Sucker A, Schadendorf D, Tsirigos A, Schalper KA, Velcheti V, Huang HY, Jin Y, Ji H, Poirier JT, Li F, Wong KK. Targeting the Atf7ip-Setdb1 Complex Augments Antitumor Immunity by Boosting Tumor Immunogenicity. Cancer Immunol Res 2021; 9:1298-1315. [PMID: 34462284 PMCID: PMC9414288 DOI: 10.1158/2326-6066.cir-21-0543] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/20/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023]
Abstract
Substantial progress has been made in understanding how tumors escape immune surveillance. However, few measures to counteract tumor immune evasion have been developed. Suppression of tumor antigen expression is a common adaptive mechanism that cancers use to evade detection and destruction by the immune system. Epigenetic modifications play a critical role in various aspects of immune invasion, including the regulation of tumor antigen expression. To identify epigenetic regulators of tumor antigen expression, we established a transplantable syngeneic tumor model of immune escape with silenced antigen expression and used this system as a platform for a CRISPR-Cas9 suppressor screen for genes encoding epigenetic modifiers. We found that disruption of the genes encoding either of the chromatin modifiers activating transcription factor 7-interacting protein (Atf7ip) or its interacting partner SET domain bifurcated histone lysine methyltransferase 1 (Setdb1) in tumor cells restored tumor antigen expression. This resulted in augmented tumor immunogenicity concomitant with elevated endogenous retroviral (ERV) antigens and mRNA intron retention. ERV disinhibition was associated with a robust type I interferon response and increased T-cell infiltration, leading to rejection of cells lacking intact Atf7ip or Setdb1. ATF7IP or SETDB1 expression inversely correlated with antigen processing and presentation pathways, interferon signaling, and T-cell infiltration and cytotoxicity in human cancers. Our results provide a rationale for targeting Atf7ip or Setdb1 in cancer immunotherapy.
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Affiliation(s)
- Hai Hu
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Alireza Khodadadi-Jamayran
- Division of Advanced Research Technologies, Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, New York
| | - Igor Dolgalev
- Division of Advanced Research Technologies, Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, New York.,Department of Pathology, NYU School of Medicine, New York, New York
| | - Hyunwoo Cho
- Division of Advanced Research Technologies, Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, New York.,Department of Pathology, NYU School of Medicine, New York, New York.,Department of Radiation Oncology, NYU School of Medicine, New York, New York
| | - Sana Badri
- Department of Pathology, NYU School of Medicine, New York, New York
| | | | - Briana Zeck
- Department of Pathology, NYU School of Medicine, New York, New York
| | | | - Catríona M. Dowling
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York.,School of Medicine, University of Limerick, Limerick, Ireland
| | - Kristen Labbe
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Jiehui Deng
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Ting Chen
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Hua Zhang
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Paul Zappile
- Division of Advanced Research Technologies, Genome Technology Center, NYU School of Medicine, New York, New York
| | - Ze Chen
- Department of Medicine, NYU School of Medicine, New York
| | | | - Angeliki Karatza
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Han Han
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Michela Ranieri
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Sittinon Tang
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - George Jour
- Department of Pathology, NYU School of Medicine, New York, New York
| | - Iman Osman
- Department of Dermatology, NYU School of Medicine, New York, New York
| | - Antje Sucker
- Department of Dermatology, University Hospital, Essen, Germany
| | | | - Aristotelis Tsirigos
- Division of Advanced Research Technologies, Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, New York.,Department of Pathology, NYU School of Medicine, New York, New York
| | - Kurt A. Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Vamsidhar Velcheti
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Hsin-yi Huang
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Yujuan Jin
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Hongbin Ji
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - John T. Poirier
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York
| | - Fei Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Corresponding Authors: Kwok-Kin Wong, Perlmutter Cancer Center, New York University Langone Medical Center, NYU School of Medicine, 550 1st Avenue, Smilow 1011, New York, NY 10016. Phone: 212-263-9203; E-mail: ; and Fei Li, Department of Pathology, School of Basic Medical Sciences, Fudan University, Room 208, East Building 1, 131 Dong'an Road, Xuhui District, Shanghai 200032, China. Phone: 86 15202100163; E-mail:
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York.,Corresponding Authors: Kwok-Kin Wong, Perlmutter Cancer Center, New York University Langone Medical Center, NYU School of Medicine, 550 1st Avenue, Smilow 1011, New York, NY 10016. Phone: 212-263-9203; E-mail: ; and Fei Li, Department of Pathology, School of Basic Medical Sciences, Fudan University, Room 208, East Building 1, 131 Dong'an Road, Xuhui District, Shanghai 200032, China. Phone: 86 15202100163; E-mail:
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Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer. Sci Rep 2021; 11:17346. [PMID: 34462486 PMCID: PMC8405634 DOI: 10.1038/s41598-021-96844-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.
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45
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Jay A, Reitz D, Namekawa SH, Heyer WD. Cancer testis antigens and genomic instability: More than immunology. DNA Repair (Amst) 2021; 108:103214. [PMID: 34481156 PMCID: PMC9196322 DOI: 10.1016/j.dnarep.2021.103214] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 12/29/2022]
Abstract
Cancer testis antigens or genes (CTA, CTG) are predominantly expressed in adult testes while silenced in most or all somatic tissues with sporadic expression in many human cancers. Concerted misexpression of numerous CTA/CTGs is rarely observed. This finding argues against the germ cell theory of cancer. A surprising number of CTA/CTGs are involved in meiotic chromosome metabolism and specifically in meiotic recombination. Recent discoveries with a group of CTGs established that their misexpression in somatic cells results in genomic instability by interfering with homologous recombination (HR), a DNA repair pathway for complex DNA damage such as DNA double-stranded breaks, interstrand crosslinks, and single-stranded DNA gaps. HR-deficient tumors have specific vulnerabilities and show synthetic lethality with inhibition of polyADP-ribose polymerase, opening the possibility that expression of CTA/CTGs that result in an HR-defect could be used as an additional biomarker for HR status. Here, we review the repertoire of CTA/CTGs focusing on a cohort that functions in meiotic chromosome metabolism by interrogating relevant cancer databases and discussing recent discoveries.
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Affiliation(s)
- Ash Jay
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, 95616-8665, USA; Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, 95616-8665, USA.
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46
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Cancer-Testis Antigens in Triple-Negative Breast Cancer: Role and Potential Utility in Clinical Practice. Cancers (Basel) 2021; 13:cancers13153875. [PMID: 34359776 PMCID: PMC8345750 DOI: 10.3390/cancers13153875] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer cells commonly express tumour-associated antigens that can induce immune responses to eradicate the tumour. Triple-negative breast cancer (TNBC) is a form of breast cancer lacking the expression of hormone receptors and cerbB2 (HER2) and tends to be more aggressive and associated with poorer prognoses due to the limited treatment options. Characterisation of biomarkers or treatment targets is thus of great significance in revealing additional therapeutic options. Cancer-testis antigens (CTAs) are tumour-associated antigens that have garnered strong attention as potential clinical biomarkers in targeted immunotherapy due to their cancer-restricted expressions and robust immunogenicity. Previous clinical studies reported that CTAs correlated with negative hormonal status, advanced tumour behaviour and a poor prognosis in a variety of cancers. Various studies also demonstrated the oncogenic potential of CTAs in cell proliferation by inhibiting cell death and inducing metastasis. Multiple clinical trials are in progress to evaluate the role of CTAs as treatment targets in various cancers. CTAs hold great promise as potential treatment targets and biomarkers in cancer, and further research could be conducted on elucidating the mechanism of actions of CTAs in breast cancer or combination therapy with other immune modulators. In the current review, we summarise the current understandings of CTAs in TNBC, addressing the role and utility of CTAs in TNBC, as well as discussing the potential applications and advantage of incorporating CTAs in clinical practise.
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Jiang X, Wen J, Paver E, Wu YH, Sun G, Bullman A, Dahlstrom JE, Tremethick DJ, Soboleva TA. H2A.B is a cancer/testis factor involved in the activation of ribosome biogenesis in Hodgkin lymphoma. EMBO Rep 2021; 22:e52462. [PMID: 34350706 DOI: 10.15252/embr.202152462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Testis-specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin lymphoma (HL) samples showed that the ectopic expression of the eutherian testis-specific histone variant H2A.B is an inherent feature of HL. In experiments using two HL cell lines derived from different subtypes of HL, H2A.B knockdown inhibited cell proliferation. H2A.B was enriched in both nucleoli of these HL cell lines and primary HL samples. We found that H2A.B enhanced ribosomal DNA (rDNA) transcription, was enriched at the rDNA promoter and transcribed regions, and interacted with RNA Pol I. Depletion of H2A.B caused the loss of RNA Pol I from rDNA chromatin. Remarkably, H2A.B was also required for high levels of ribosomal protein gene expression being located at the transcriptional start site and within the gene body. H2A.B knockdown reduced gene body chromatin accessibility of active RNA Pol II genes concurrent with a decrease in transcription. Taken together, our data show that in HL H2A.B has acquired a new function, the ability to increase ribosome biogenesis.
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Affiliation(s)
- Xuanzhao Jiang
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Jiayu Wen
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Elizabeth Paver
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Yu-Huan Wu
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Gege Sun
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Amanda Bullman
- Department of Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra, ACT, Australia
| | - Jane E Dahlstrom
- Department of Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra, ACT, Australia.,Australian National University Medical School, The Australian National University, Canberra, ACT, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Tatiana A Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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Alzahrani FA, Hawsawi YM, Altayeb HN, Alsiwiehri NO, Alzahrani OR, Alatwi HE, Al‐Amer OM, Alomar S, Mansour L. In silico modeling of the interaction between TEX19 and LIRE1, and analysis of TEX19 gene missense SNPs. Mol Genet Genomic Med 2021; 9:e1707. [PMID: 34036740 PMCID: PMC8372073 DOI: 10.1002/mgg3.1707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Testis expressed 19 (TEX19) is a specific human stem cell gene identified as cancer-testis antigen (CTA), which emerged as a potential therapeutic drug target. TEX19.1, a mouse paralog of human TEX19, can interact with LINE-1 retrotransposable element ORF1 protein (LIRE1) and subsequently restrict mobilization of LINE-1 elements in the genome. AIM This study aimed to predict the interaction of TEX19 with LIRE1 and analyze TEX19 missense polymorphisms. TEX19 model was generated using I-TASSER and the interaction between TEX19 and LIRE1 was studied using the HADDOCK software. METHODS The stability of the docking formed complex was studied through the molecular dynamic simulation using GROMACS. Missense SNPs (n=102) of TEX19 were screened for their potential effects on protein structure and function using different software. RESULTS Outcomes of this study revealed amino acids that potentially stabilize the predicted interaction interface between TEX19 and LIRE1. Of these SNPs, 37 were predicted to play a probably damaging role for the protein, three of them (F35S, P61R, and E55L) located at the binding site of LIRE1 and could disturb this binding affinity. CONCLUSION This information can be verified by further in vitro and in vivo experimentations and could be exploited for potential therapeutic targets.
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Affiliation(s)
- Faisal A. Alzahrani
- Department of BiochemistryFaculty of ScienceEmbryonic Stem Cell UnitKing Fahad Center for Medical ResearchKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Yousef MohammedRabaa Hawsawi
- Research Center at King Faisal Specialist Hospital and Research CenterJeddahSaudi Arabia
- College of MedicineAl‐Faisal UniversityRiyadhSaudi Arabia
| | - Hisham N. Altayeb
- Department of BiochemistryFaculty of ScienceEmbryonic Stem Cell UnitKing Fahad Center for Medical ResearchKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Naif O. Alsiwiehri
- Department of Clinical Laboratory ScienceFaculty of Applied Medical ScienceTaif UniversityTaifSaudi Arabia
| | - Othman R. Alzahrani
- Department of BiologyFaculty of SciencesUniversity of TabukTabukSaudi Arabia
- Genome and Biotechnology UnitFaculty of ScienceUniversity of TabukTabukSaudi Arabia
| | - Hanan E. Alatwi
- Department of BiologyFaculty of SciencesUniversity of TabukTabukSaudi Arabia
- Genome and Biotechnology UnitFaculty of ScienceUniversity of TabukTabukSaudi Arabia
| | - Osama M. Al‐Amer
- Genome and Biotechnology UnitFaculty of ScienceUniversity of TabukTabukSaudi Arabia
- Department of Medical Laboratory TechnologyFaculty of Applied Medical SciencesUniversity of TaboukTabukSaudi Arabia
| | - Suliman Alomar
- Doping Research ChairDepartment of ZoologyCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Lamjed Mansour
- Doping Research ChairDepartment of ZoologyCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia
- Department of ZoologyCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia
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Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, Kapolou K, Walz JS, Velz J, Moch H, Regli L, Silginer M, Weller M, Löffler MW, Erhard F, Schlosser A, Kohlbacher O, Stevanović S, Rammensee HG, Neidert MC. HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. J Immunother Cancer 2021; 9:e002071. [PMID: 33858848 PMCID: PMC8054196 DOI: 10.1136/jitc-2020-002071] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. METHODS Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. RESULTS The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. CONCLUSION Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org .
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Affiliation(s)
- Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Daniel Johannes Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Linus Backert
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - András Szolek
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Philipp Wagner
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Sabine Matovina
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Konstantina Kapolou
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Juliane Sarah Walz
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Julia Velz
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Manuela Silginer
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University of Hospital Tübingen, Tübingen, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Bayern, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center - Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Marian Christoph Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zurich, Switzerland
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Dwivedi SKD, Rao G, Dey A, Mukherjee P, Wren JD, Bhattacharya R. Small Non-Coding-RNA in Gynecological Malignancies. Cancers (Basel) 2021; 13:1085. [PMID: 33802524 PMCID: PMC7961667 DOI: 10.3390/cancers13051085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022] Open
Abstract
Gynecologic malignancies, which include cancers of the cervix, ovary, uterus, vulva, vagina, and fallopian tube, are among the leading causes of female mortality worldwide, with the most prevalent being endometrial, ovarian, and cervical cancer. Gynecologic malignancies are complex, heterogeneous diseases, and despite extensive research efforts, the molecular mechanisms underlying their development and pathology remain largely unclear. Currently, mechanistic and therapeutic research in cancer is largely focused on protein targets that are encoded by about 1% of the human genome. Our current understanding of 99% of the genome, which includes noncoding RNA, is limited. The discovery of tens of thousands of noncoding RNAs (ncRNAs), possessing either structural or regulatory functions, has fundamentally altered our understanding of genetics, physiology, pathophysiology, and disease treatment as they relate to gynecologic malignancies. In recent years, it has become clear that ncRNAs are relatively stable, and can serve as biomarkers for cancer diagnosis and prognosis, as well as guide therapy choices. Here we discuss the role of small non-coding RNAs, i.e., microRNAs (miRs), P-Element induced wimpy testis interacting (PIWI) RNAs (piRNAs), and tRNA-derived small RNAs in gynecological malignancies, specifically focusing on ovarian, endometrial, and cervical cancer.
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Affiliation(s)
- Shailendra Kumar Dhar Dwivedi
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Geeta Rao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
| | - Anindya Dey
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
| | - Priyabrata Mukherjee
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (G.R.); (P.M.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D. Wren
- Biochemistry and Molecular Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (S.K.D.D.); (A.D.)
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
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