1
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Zhang YT, Shen G, Zhuo LC, Yang X, Wang SY, Ruan TC, Jiang C, Wang X, Wang Y, Yang YH, Shen Y. Novel variations in TENT5D lead to teratozoospermia in infertile patients. Andrology 2024. [PMID: 38228861 DOI: 10.1111/andr.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024]
Abstract
PURPOSE Teratozoospermia is the main pathogenic factor of male infertility. However, the genetic etiology of teratozoospermia is largely unknown. This study aims to clarify the relationship between novel variations in TENT5D and teratozoospermia in infertile patients. MATERIALS AND METHODS Two infertile patients were enrolled. Routine semen analysis of patients and normal controls was conducted with the WHO guidelines. Whole-exome sequencing (WES) was conducted to identify pathogenic variants in the two patients. Morphology and ultrastructure analysis of spermatozoa in the two patients was determined by Papanicolaou staining, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The functional effect of the identified variants was analyzed by immunofluorescence staining and western blotting. The expression of TENT5D in different germ cells was detected by immunofluorescence staining. RESULTS Two new hemizygous variations, c.101C > T (p.P34L) and c.125A > T (p.D42V), in TENT5D were detected in two patients with male infertility. Morphology analysis showed abnormalities in spermatozoa morphology in the two patients, including multiple heads, headless, multiple tails, coiled, and/or bent flagella. Ultrastructure analysis showed that most of the spermatozoa exhibited missing or irregularly arranged '9+2' structures. Further functional experiments confirmed the abrogated TENT5D protein expression in patients. In addition, both p.P34L and p.D42V substitutions resulted in a conformational change of the TENT5D protein. We precisely analyzed the subcellular localization of TENT5D in germ cells in humans and mice. And we found that TENT5D was predominantly detected in the head and flagellum of elongating spermatids and epididymal spermatozoa. CONCLUSIONS Our results showed further evidence of a relationship between TENT5D mutation and human male infertility, providing new genetic insight for use in the diagnosis and treatment of male infertility.
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Affiliation(s)
- Ying-Teng Zhang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Gan Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Liang-Chai Zhuo
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xue Yang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Su-Yan Wang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Tie-Chao Ruan
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chuan Jiang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Yi-Hong Yang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
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Mancino M, Lai G, De Grossi F, Cuomo A, Manganaro L, Butta GM, Ferrari I, Vicenzi E, Poli G, Pesce E, Oliveto S, Biffo S, Manfrini N. FAM46C Is an Interferon-Stimulated Gene That Inhibits Lentiviral Particle Production by Modulating Autophagy. Microbiol Spectr 2023; 11:e0521122. [PMID: 37358411 PMCID: PMC10434054 DOI: 10.1128/spectrum.05211-22] [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: 12/22/2022] [Accepted: 06/02/2023] [Indexed: 06/27/2023] Open
Abstract
FAM46C is a multiple myeloma (MM) tumor suppressor whose function is only starting to be elucidated. We recently showed that in MM cells FAM46C triggers apoptosis by inhibiting autophagy and altering intracellular trafficking and protein secretion. To date, both a physiological characterization of FAM46C role and an assessment of FAM46C-induced phenotypes outside of MM are lacking. Preliminary reports suggested an involvement of FAM46C with regulation of viral replication, but this was never confirmed. Here, we show that FAM46C is an interferon-stimulated gene and that the expression of wild-type FAM46C in HEK-293T cells, but not of its most frequently found mutant variants, inhibits the production of both HIV-1-derived and HIV-1 lentiviruses. We demonstrate that this effect does not require transcriptional regulation and does not depend on inhibition of either global or virus-specific translation but rather mostly relies on FAM46C-induced deregulation of autophagy, a pathway that we show to be required for efficient lentiviral particle production. These studies not only provide new insights on the physiological role of the FAM46C protein but also could help in implementing more efficient antiviral strategies on one side and lentiviral particle production approaches on the other. IMPORTANCE FAM46C role has been thoroughly investigated in MM, but studies characterizing its role outside of the tumoral environment are still lacking. Despite the success of antiretroviral therapy in suppressing HIV load to undetectable levels, there is currently no HIV cure, and treatment is lifelong. Indeed, HIV continues to be a major global public health issue. Here, we show that FAM46C expression in HEK-293T cells inhibits the production of both HIV and HIV-derived lentiviruses. We also demonstrate that such inhibitory effect relies, at least in part, on the well-established regulatory role that FAM46C exerts on autophagy. Deciphering the molecular mechanism underlying this regulation will not only facilitate the understanding of FAM46C physiological role but also give new insights on the interplay between HIV and the cellular environment.
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Affiliation(s)
- Marilena Mancino
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Giacomo M. Butta
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Ivan Ferrari
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Guido Poli
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Stefania Oliveto
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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3
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Donizetti A, Venditti M, Arcaniolo D, Aliperti V, Carrese AM, De Sio M, Minucci S, Caraglia M, Aniello F. The long non-coding RNA transcript, LOC100130460 (CAND1.11) gene, encodes a novel protein highly expressed in cancer cells and tumor human testis tissues. Cancer Biomark 2023; 38:343-353. [PMID: 37661873 DOI: 10.3233/cbm-230160] [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] [Indexed: 09/05/2023]
Abstract
BACKGROUND Testis-specific genes encoding for long non-coding RNA (lncRNA) have been detected in several cancers; many produce proteins with restricted or aberrant expression patterns in normal or cancer tissues. OBJECTIVE To characterize new lncRNA involved in normal and/or pathological differentiation of testicular cells. METHODS Using bioinformatics analysis, we found that lncRNA LOC100130460 (CAND1.11) is expressed in normal and tumor testis; its expression was assessed in several human cell lines by qRT-PCR. CAND1.11 protein, produced by a single nucleotide mutation, was studied by western blot and immunofluorescence analysis on normal, classic seminoma, and Leydig cell tumor testicular tissues. RESULTS CAND1.11 gene is primate-specific; its expression was low in SH-SY5Y cells and increased when differentiated with retinoic acid treatment. CAND1.11 expression in PC3 cells was higher than in PNT2 cells. CAND1.11 protein is present in the human testis and overexpressed in testicular cancer tissues. CONCLUSIONS This report is one of the few providing evidence that a lncRNA produces a protein expressed in normal human tissues and overexpressed in several testicular cancers, suggesting its involvement in regulating cell proliferation and differentiation. Although further studies are needed to validate the results, our data indicate that CAND1.11 could be a potential new prognostic biomarker to use in proliferation and cancer.
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Affiliation(s)
- Aldo Donizetti
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Massimo Venditti
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Davide Arcaniolo
- Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Vincenza Aliperti
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Anna Maria Carrese
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
| | - Marco De Sio
- Dipartimento della Donna, del Bambino e di Chirurgia Generale e Specialistica, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Sergio Minucci
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Michele Caraglia
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Francesco Aniello
- Dipartimento di Biologia, Università di Napoli "Federico II", Napoli, Italy
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Liang T, Ye X, Yan D, Deng C, Li Z, Tian B. FAM46B Promotes Apoptosis and Inhibits Glycolysis of Prostate Cancer Through Inhibition of the MYC-LDHA Axis. Onco Targets Ther 2020; 13:8771-8782. [PMID: 32943883 PMCID: PMC7478375 DOI: 10.2147/ott.s258724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022] Open
Abstract
Objective Increased dependence on glycolysis is a known element of cancer. This study was designed to examine critical glycolysis components including transcription factor MYC and its downstream target lactate dehydrogenase A (LDHA), potential upstream regulators of glycolysis such as family with sequence similarity 46 member B (FAM46B), and the impact of the abundance of these proteins on apoptosis and glycolysis in prostate cancer. Materials and Methods A total of 70 primary prostate cancer patient samples were compared to normal tissues for FAM46B and LDHA expression and the corresponding patients’ survival was monitored for 60 months. Prostate cancer cell lines were employed for protein expression manipulation, glucose uptake and LDH assays, and apoptosis measurements. A xenograft mouse model was used to quantify the role of FAM46B and LDHA on tumor growth in vivo. Results FAM46B expression was reduced in prostate tumor tissue compared to normal tissue and prostate cancer patients who expressed low amounts of FAM46B had shortened average lifespans compared to those who expressed higher amounts of FAM46B (p=0.008). FAM46B overexpression reduced glucose uptake, decreased LDH activity, and induced apoptosis in prostate cancer cell lines while FAM46B shRNA increased MYC levels in a non-malignant prostate cell line (P69). Conversely, forced expression of LDHA in LNCaP cells produced an increase in glycolysis markers with a corresponding decrease in apoptosis. FAM46B-overexpressing xenografts had starkly blunted growth which was restored with co-overexpression of LDHA. Conclusion FAM46B plays a central role in regulating glycolysis and apoptosis in prostate cancer and operates through the regulation of LDHA via MYC. FAM46B’s keystone status in prostate cancer makes it a potential, robust biomarker for prostate cancer prognosis and a promising therapeutic target.
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Affiliation(s)
- Tao Liang
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Xuxiao Ye
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Dongliang Yan
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Chao Deng
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Zuowei Li
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Binqiang Tian
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
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5
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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6
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A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat Rev Mol Cell Biol 2020; 21:542-556. [PMID: 32483315 DOI: 10.1038/s41580-020-0246-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
Abstract
RNA tailing, or the addition of non-templated nucleotides to the 3' end of RNA, is the most frequent and conserved type of RNA modification. The addition of tails and their composition reflect RNA maturation stages and have important roles in determining the fate of the modified RNAs. Apart from canonical poly(A) polymerases, which add poly(A) tails to mRNAs in a transcription-coupled manner, a family of terminal nucleotidyltransferases (TENTs), including terminal uridylyltransferases (TUTs), modify RNAs post-transcriptionally to control RNA stability and activity. The human genome encodes 11 different TENTs with distinct substrate specificity, intracellular localization and tissue distribution. In this Review, we discuss recent advances in our understanding of non-canonical RNA tails, with a focus on the functions of human TENTs, which include uridylation, mixed tailing and post-transcriptional polyadenylation of mRNAs, microRNAs and other types of non-coding RNA.
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7
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Ma L, He H, Jiang K, Jiang P, He H, Feng S, Chen K, Shao J, Deng G. FAM46C inhibits cell proliferation and cell cycle progression and promotes apoptosis through PTEN/AKT signaling pathway and is associated with chemosensitivity in prostate cancer. Aging (Albany NY) 2020; 12:6352-6369. [PMID: 32283544 PMCID: PMC7185131 DOI: 10.18632/aging.103030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/23/2020] [Indexed: 04/11/2023]
Abstract
Family with sequence similarity 46 member C (FAM46C) is a non-canonical poly(A) polymerase that is associated with tumorigenesis. However, its role in prostate cancer development is not fully understood. Herein, we determined expression pattern of FAM46C in prostate cancer and further identified its effect on the tumorigenesis and chemosensitivity. FAM46C expression was decreased in prostate cancer tissues and cell lines compared with corresponding controls. FAM46C expression was significantly associated with the Gleason score, tumor size and overall survival. FAM46C knockdown in 22RV1 and DU145 cells significantly inhibited apoptosis and promoted cell proliferation and cell cycle progression as well as activation of AKT. FAM46C overexpression had an inverse effect in DU145 cells and inhibited tumor growth in vivo. FAM46C inhibited cell proliferation and cell cycle progression and induced apoptosis via the PTEN/AKT signaling pathway. FAM46C promoted PTEN expression through inhibiting PTEN ubiquitination. The prostate cancer cells and patient-derived xenograft (PDX) mice with high-FAM46C-expressing demonstrated an enhanced chemosensitivity to docetaxel. These findings suggest that FAM46C control cell proliferation, cell cycle and apoptosis through PTEN/AKT signaling pathway and is associated with chemosensitivity of prostate cancer. Modulation of their levels may offer a new approach for improving anti-tumor efficacy for chemotherapeutic agents in prostate cancer.
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Affiliation(s)
- Libin Ma
- Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, Zhejiang, China
| | - Huadong He
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Kang Jiang
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Peiwu Jiang
- Surgical Department I, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou 310007, Zhejiang, China
| | - Han He
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Shengjia Feng
- Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou 310006, Zhejiang, China
| | - Kean Chen
- Department of Urology, The Second Hospital of Jiaxing, Jiaxing 314001, Zhejiang, China
| | - Jia Shao
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
| | - Gang Deng
- Department of Urology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, Zhejiang, China
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Salichos L, Meyerson W, Warrell J, Gerstein M. Estimating growth patterns and driver effects in tumor evolution from individual samples. Nat Commun 2020; 11:732. [PMID: 32024824 PMCID: PMC7002450 DOI: 10.1038/s41467-020-14407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/26/2019] [Indexed: 01/01/2023] Open
Abstract
Tumors accumulate thousands of mutations, and sequencing them has given rise to methods for finding cancer drivers via mutational recurrence. However, these methods require large cohorts and underperform for low recurrence. Recently, ultra-deep sequencing has enabled accurate measurement of VAFs (variant-allele frequencies) for mutations, allowing the determination of evolutionary trajectories. Here, based solely on the VAF spectrum for an individual sample, we report on a method that identifies drivers and quantifies tumor growth. Drivers introduce perturbations into the spectrum, and our method uses the frequency of hitchhiking mutations preceding a driver to measure this. As validation, we use simulation models and 993 tumors from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium with previously identified drivers. Then we apply our method to an ultra-deep sequenced acute myeloid leukemia (AML) tumor and identify known cancer genes and additional driver candidates. In summary, our framework presents opportunities for personalized driver diagnosis using sequencing data from a single individual.
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Affiliation(s)
- Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - William Meyerson
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Computer Science, Yale University, New Haven, CT, 06520, USA.
- Center for Biomedical Data Science, Yale University, New Haven, CT, 06520, USA.
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9
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Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M. Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment. J Immunother Cancer 2019; 7:309. [PMID: 31735170 PMCID: PMC6859637 DOI: 10.1186/s40425-019-0769-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Patient derived organoids (PDOs) can be established from colorectal cancers (CRCs) as in vitro models to interrogate cancer biology and its clinical relevance. We applied mass spectrometry (MS) immunopeptidomics to investigate neoantigen presentation and whether this can be augmented through interferon gamma (IFNγ) or MEK-inhibitor treatment. METHODS Four microsatellite stable PDOs from chemotherapy refractory and one from a treatment naïve CRC were expanded to replicates with 100 million cells each, and HLA class I and class II peptide ligands were analyzed by MS. RESULTS We identified an average of 9936 unique peptides per PDO which compares favorably against published immunopeptidomics studies, suggesting high sensitivity. Loss of heterozygosity of the HLA locus was associated with low peptide diversity in one PDO. Peptides from genes without detectable expression by RNA-sequencing were rarely identified by MS. Only 3 out of 612 non-silent mutations encoded for neoantigens that were detected by MS. In contrast, computational HLA binding prediction estimated that 304 mutations could generate neoantigens. One hundred ninety-six of these were located in expressed genes, still exceeding the number of MS-detected neoantigens 65-fold. Treatment of four PDOs with IFNγ upregulated HLA class I expression and qualitatively changed the immunopeptidome, with increased presentation of IFNγ-inducible genes. HLA class II presented peptides increased dramatically with IFNγ treatment. MEK-inhibitor treatment showed no consistent effect on HLA class I or II expression or the peptidome. Importantly, no additional HLA class I or II presented neoantigens became detectable with any treatment. CONCLUSIONS Only 3 out of 612 non-silent mutations encoded for neoantigens that were detectable by MS. Although MS has sensitivity limits and biases, and likely underestimated the true neoantigen burden, this established a lower bound of the percentage of non-silent mutations that encode for presented neoantigens, which may be as low as 0.5%. This could be a reason for the poor responses of non-hypermutated CRCs to immune checkpoint inhibitors. MEK-inhibitors recently failed to improve checkpoint-inhibitor efficacy in CRC and the observed lack of HLA upregulation or improved peptide presentation may explain this.
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Affiliation(s)
- Alice Newey
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Beatrice Griffiths
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Justine Michaux
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Hui Song Pak
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Andrew Woolston
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Maria Semiannikova
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Georgia Spain
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Louise J. Barber
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Nik Matthews
- Tumour Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
| | - Sheela Rao
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - David Watkins
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - Ian Chau
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - George Coukos
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Naureen Starling
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - David Cunningham
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
| | - Michal Bassani-Sternberg
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland
| | - Marco Gerlinger
- Translational Oncogenomics Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB UK
- GI Cancer Unit, The Royal Marsden Hospital, Fulham Road, London, SW3 6JJ UK
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10
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Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ, Liang J. Distinct genome‐wide alternative polyadenylation during the response to silicon availability in the marine diatom
Thalassiosira pseudonana. THE PLANT JOURNAL 2019; 99:67-80. [PMID: 30844106 DOI: 10.1111/tpj.14309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/15/2019] [Accepted: 02/27/2019] [Indexed: 05/28/2023]
Affiliation(s)
- Haihui Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Peng Wang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Xiaohui Wu
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Xiaoxuan Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Guoli Ji
- Department of Automation Xiamen University Xiamen Fujian 361005 China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
| | - Yahui Gao
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and Ecology Xiamen University Xiamen Fujian 361102 China
- Graduate College of Biomedical Sciences Western University of Health Sciences Pomona CA 91766 USA
| | - Junrong Liang
- School of Life Sciences Xiamen University Xiamen Fujian 361102 China
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11
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Astaneh M, Dashti S, Esfahani ZT. Humoral immune responses against cancer-testis antigens in human malignancies. Hum Antibodies 2019; 27:237-240. [PMID: 31006681 DOI: 10.3233/hab-190377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND Cancer-testis antigens (CTAs) are a class of cancer antigens with extensive expression in human cancers. Many researchers have detected antibody responses against these tumor antigens in serum of cancer patients. OBJECTIVES To evaluate the relevance of humoral immune responses against CTAs in clinical outcome of cancer patientsMETHODS: We searched PubMed/Medline with the key words cancer-testis antigen, antibody, humoral response and cancer. RESULTS Humoral immune responses against CTAs have been detected in several human malignancies including skin, breast, brain and ovarian cancers. Some studies have shown associations between the presence of these responses in patients and patients' survival. CONCLUSION Humoral immune responses against CTAs are putative biomarkers for cancer detection and follow-up.
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12
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Warkocki Z, Liudkovska V, Gewartowska O, Mroczek S, Dziembowski A. Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0162. [PMID: 30397099 PMCID: PMC6232586 DOI: 10.1098/rstb.2018.0162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Vladyslava Liudkovska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Olga Gewartowska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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13
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Faramarzi S, Ghafouri-Fard S. Expression analysis of cancer-testis genes in prostate cancer reveals candidates for immunotherapy. Immunotherapy 2018; 9:1019-1034. [PMID: 28971747 DOI: 10.2217/imt-2017-0083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer is a prevalent disorder among men with a heterogeneous etiological background. Several molecular events and signaling perturbations have been found in this disorder. Among genes whose expressions have been altered during the prostate cancer development are cancer-testis antigens (CTAs). This group of antigens has limited expression in the normal adult tissues but aberrant expression in cancers. This property provides them the possibility to be used as cancer biomarkers and immunotherapeutic targets. Several CTAs have been shown to be immunogenic in prostate cancer patients and some of the have entered clinical trials. Based on the preliminary data obtained from these trials, it is expected that CTA-based therapeutic options are beneficial for at least a subset of prostate cancer patients.
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Affiliation(s)
- Sepideh Faramarzi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Kuchta K, Muszewska A, Knizewski L, Steczkiewicz K, Wyrwicz LS, Pawlowski K, Rychlewski L, Ginalski K. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. Nucleic Acids Res 2016; 44:3534-48. [PMID: 27060136 PMCID: PMC4857005 DOI: 10.1093/nar/gkw222] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/22/2016] [Indexed: 12/22/2022] Open
Abstract
FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are thought to be involved in several diseases, with FAM46C reported as a causal driver of multiple myeloma; however, their exact functions remain unknown. By using a combination of various bioinformatics analyses (e.g. domain architecture, cellular localization) and exhaustive literature and database searches (e.g. expression profiles, protein interactors), we classified FAM46 proteins as active non-canonical poly(A) polymerases, which modify cytosolic and/or nuclear RNA 3′ ends. These proteins may thus regulate gene expression and probably play a critical role during cell differentiation. A detailed analysis of sequence and structure diversity of known NTases possessing PAP/OAS1 SBD domain, combined with state-of-the-art comparative modelling, allowed us to identify potential active site residues responsible for catalysis and substrate binding. We also explored the role of single point mutations found in human cancers and propose that FAM46 genes may be involved in the development of other major malignancies including lung, colorectal, hepatocellular, head and neck, urothelial, endometrial and renal papillary carcinomas and melanoma. Identification of these novel enzymes taking part in RNA metabolism in eukaryotes may guide their further functional studies.
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Affiliation(s)
- Krzysztof Kuchta
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Anna Muszewska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Lukasz Knizewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Lucjan S Wyrwicz
- Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
| | - Krzysztof Pawlowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02-787 Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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15
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Exome sequencing identifies a nonsense mutation in Fam46a associated with bone abnormalities in a new mouse model for skeletal dysplasia. Mamm Genome 2016; 27:111-21. [PMID: 26803617 DOI: 10.1007/s00335-016-9619-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/04/2016] [Indexed: 12/31/2022]
Abstract
We performed exome sequencing for mutation discovery of an ENU (N-ethyl-N-nitrosourea)-derived mouse model characterized by significant elevated plasma alkaline phosphatase (ALP) activities in female and male mutant mice, originally named BAP014 (bone screen alkaline phosphatase #14). We identified a novel loss-of-function mutation within the Fam46a (family with sequence similarity 46, member A) gene (NM_001160378.1:c.469G>T, NP_001153850.1:p.Glu157*). Heterozygous mice of this mouse line (renamed Fam46a (E157*Mhda)) had significantly high ALP activities and apparently no other differences in morphology compared to wild-type mice. In contrast, homozygous Fam46a (E157*Mhda) mice showed severe morphological and skeletal abnormalities including short stature along with limb, rib, pelvis, and skull deformities with minimal trabecular bone and reduced cortical bone thickness in long bones. ALP activities of homozygous mutants were almost two-fold higher than in heterozygous mice. Fam46a is weakly expressed in most adult and embryonic tissues with a strong expression in mineralized tissues as calvaria and femur. The FAM46A protein is computationally predicted as a new member of the superfamily of nucleotidyltransferase fold proteins, but little is known about its function. Fam46a (E157*Mhda) mice are the first mouse model for a mutation within the Fam46a gene.
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16
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Ghafouri-Fard S, Shamsi R, Seifi-Alan M, Javaheri M, Tabarestani S. Cancer-testis genes as candidates for immunotherapy in breast cancer. Immunotherapy 2014; 6:165-79. [PMID: 24491090 DOI: 10.2217/imt.13.165] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cancer-testis (CT) antigens are tumor-associated antigens attracting immunologists for their possible application in the immunotherapy of cancer. Several clinical trials have assessed their therapeutic potentials in cancer patients. Breast cancers, especially triple-negative cancers are among those with significant expression of CT genes. Identification of CT genes with high expression in cancer patients is the prerequisite for any immunotherapeutic approach. CT genes have gained attention not only for immunotherapy of cancer patients, but also for immunoprevention in high-risk individuals. Many CT genes have proved to be immunogenic in breast cancer patients suggesting the basis for the development of polyvalent vaccines.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran 19857-17443, Iran
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17
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A Panel of Cancer Testis Antigens and Clinical Risk Factors to Predict Metastasis in Colorectal Cancer. J Biomark 2014; 2014:272683. [PMID: 26317029 PMCID: PMC4437385 DOI: 10.1155/2014/272683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 01/30/2014] [Accepted: 01/31/2014] [Indexed: 02/01/2023] Open
Abstract
Colorectal cancer (CRC) is the third common carcinoma with a high rate of mortality worldwide and several studies have investigated some molecular and clinicopathological markers for diagnosis and prognosis of its malignant phenotypes. The aim of this study is to evaluate expression frequency of PAGE4, SCP-1, and SPANXA/D cancer testis antigen (CTA) genes as well as some clinical risk markers to predict liver metastasis of colorectal cancer patients. The expression frequency of PAGE4, SCP-1, and SPANXA/D cancer/testis antigen (CTA) genes was obtained using reverse transcription polymerase chain reaction (RT-PCR) assay in 90 colorectal tumor samples including both negative and positive liver metastasis tumors. Statistical analysis was performed to assess the association of three studied genes and clinical risk factors with CRC liver metastasis. The frequency of PAGE4 and SCP-1 genes expression was significantly higher in the primary tumours with liver metastasis when statistically compared with primary tumors with no liver metastasis (P < 0.05). Among all clinical risk factors studied, the lymph node metastasis and the depth of invasion were statistically correlated with liver metastasis of CRC patients. In addition, using multiple logistic regression, we constructed a model based on PAGE4 and lymph node metastasis to predict liver metastasis of CRC.
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18
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Conde L, Foo JN, Riby J, Liu J, Darabi H, Hjalgrim H, Bracci PM, Smedby KE, Skibola CF. X chromosome-wide association study of follicular lymphoma. Br J Haematol 2013; 162:858-62. [PMID: 23795672 DOI: 10.1111/bjh.12438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ghafouri-Fard S, Modarressi MH. Expression of cancer-testis genes in brain tumors: implications for cancer immunotherapy. Immunotherapy 2012; 4:59-75. [PMID: 22150001 DOI: 10.2217/imt.11.145] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cancer-testis (CT) genes have a restricted expression in normal tissues except testis and a wide range of tumor types. Testis is an immune-privileged site as a result of a blood barrier and lack of HLA class I expression on the surface of germ cells. Hence, if testis-specific genes are expressed in other tissues, they can be immunogenic. Expression of some CT genes in a high percentage of brain tumors makes them potential targets for immunotherapy. In addition, expression of CT genes in cancer stem cells may provide special targets for treatment of cancer recurrences and metastasis. The presence of antibodies against different CT genes in patients with advanced tumors has raised the possibility of polyvalent antitumor vaccine application.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran 19857-17443, Iran.
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20
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Liu F, Jin S, Li N, Liu X, Wang H, Li J. Comparative and functional analysis of testis-specific genes. Biol Pharm Bull 2011; 34:28-35. [PMID: 21212513 DOI: 10.1248/bpb.34.28] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The testis is the special male gonad responsible for spermatogenesis and steroidogenesis with complex gene expressions. Characterizing and comparing the testis-specific genes in different species can reveal key genes related to testis specific functions and provide supplementary information for study of human testis function. We screened testis-specific genes from Unigene libraries, total 317, 449 and 147 testis-specific genes were identified for human, mouse and rat, respectively. Ten from thirteen selected human testis-specific genes were validated exclusively expressed in the testis by reverse transcription polymerase chain reaction (RT-PCR). Systematic bioinformatics analysis showed that specific genes were mainly related to spermatogenesis and testis development process with significant Glycolysis and Pyruvate metabolism. Enrichment functions were discussed.
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Affiliation(s)
- FuJun Liu
- Shandong Research Centre for Stem Cell Engineering, Yu-Huang-Ding Hospital and Yan-Tai University, Yantai, Shandong Province 264000, PR China
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21
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Multiple autism-like behaviors in a novel transgenic mouse model. Behav Brain Res 2010; 218:29-41. [PMID: 21093492 DOI: 10.1016/j.bbr.2010.11.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 11/05/2010] [Accepted: 11/09/2010] [Indexed: 11/21/2022]
Abstract
Autism spectrum disorder (ASD) diagnoses are behaviorally based with no defined universal biomarkers, occur at a 1:110 ratio in the population, and predominantly affect males compared to females at approximately a 4:1 ratio. One approach to investigate and identify causes of ASD is to use organisms that display abnormal behavioral responses that model ASD-related impairments. This study describes a novel transgenic mouse, MALTT, which was generated using a forward genetics approach. It was determined that the transgene integrated within a non-coding region on the X chromosome. The MALTT line exhibited a complete repertoire of ASD-like behavioral deficits in all three domains required for an ASD diagnosis: reciprocal social interaction, communication, and repetitive or inflexible behaviors. Specifically, MALTT male mice showed deficits in social interaction and interest, abnormalities in pup and juvenile ultrasonic vocalization communications, and exhibited a repetitive stereotypy. Abnormalities were also observed in the domain of sensory function, a secondary phenotype prevalently associated with ASD. Mapping and expression studies suggested that the Fam46 gene family may be linked to the observed ASD-related behaviors. The MALTT line provides a unique genetic model for examining the underlying biological mechanisms involved in ASD-related behaviors.
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Huang J, Perlis RH, Lee PH, Rush AJ, Fava M, Sachs GS, Lieberman J, Hamilton SP, Sullivan P, Sklar P, Purcell S, Smoller JW. Cross-disorder genomewide analysis of schizophrenia, bipolar disorder, and depression. Am J Psychiatry 2010; 167:1254-63. [PMID: 20713499 PMCID: PMC3880556 DOI: 10.1176/appi.ajp.2010.09091335] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Family and twin studies indicate substantial overlap of genetic influences on psychotic and mood disorders. Linkage and candidate gene studies have also suggested overlap across schizophrenia, bipolar disorder, and major depressive disorder. The purpose of this study was to apply genomewide association study (GWAS) analysis to address the specificity of genetic effects on these disorders. METHOD The authors combined GWAS data from three large effectiveness studies of schizophrenia (CATIE, genotyped: N=741), bipolar disorder (STEP-BD, geno-typed: N=1,575), and major depressive disorder (STAR*D, genotyped: N=1,938) as well as from psychiatrically screened control subjects (NIMH-Genetics Repository: N=1,204). A two-stage analytic procedure involving an omnibus test of allele frequency differences among case and control groups was applied, followed by a model selection step to identify the best-fitting model of allelic effects across disorders. RESULTS The strongest result was seen for a single nucleotide polymorphism near the adrenomedullin (ADM) gene (rs6484218), with the best-fitting model indicating that the effect was specific to bipolar II disorder. Findings also revealed evidence suggesting that several genes may have effects that transcend clinical diagnostic boundaries, including variants in NPAS3 that showed pleiotropic effects across schizophrenia, bipolar disorder, and major depressive disorder. CONCLUSIONS This study provides the first genomewide significant evidence implicating variants near the ADM gene on chromosome 11p15 in psychopathology, with effects that appear to be specific to bipolar II disorder. Although genomewide significant evidence of cross-disorder effects was not detected, the results provide evidence that there are both pleiotropic and disorder-specific effects on major mental illness and illustrate an approach to dissecting the genetic basis of mood and psychotic disorders that can inform future large-scale cross-disorder GWAS analyses.
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Affiliation(s)
- Jie Huang
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Psychiatric Genetics Program in Mood and Anxiety Disorders, Massachusetts General Hospital, Boston, MA
| | - Roy H. Perlis
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Phil H. Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Psychiatric Genetics Program in Mood and Anxiety Disorders, Massachusetts General Hospital, Boston, MA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | | | - Maurizio Fava
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA
| | - Gary S. Sachs
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA
| | - Jeffrey Lieberman
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University and New York State Psychiatric Institute, New York, NY
| | - Steven P. Hamilton
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, CA
| | - Patrick Sullivan
- Departments of Genetics, Psychiatry, and Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pamela Sklar
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Shaun Purcell
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
| | - Jordan W. Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, and Psychiatric Genetics Program in Mood and Anxiety Disorders, Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Psychiatric Genetics Program in Mood and Anxiety Disorders, Massachusetts General Hospital, Boston, MA,Department of Psychiatry, Massachusetts General Hospital, Boston, MA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA
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Zhao L, Mou DC, Peng JR, Huang L, Wu ZA, Leng XS. Diagnostic value of cancer-testis antigen mRNA in peripheral blood from hepatocellular carcinoma patients. World J Gastroenterol 2010; 16:4072-8. [PMID: 20731022 PMCID: PMC2928462 DOI: 10.3748/wjg.v16.i32.4072] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To evaluate the diagnostic value of cancer-testis antigen (CTA) mRNA in peripheral blood samples from hepatocellular carcinoma (HCC) patients.
METHODS: Peripheral blood samples were taken from 90 patients with HCC before operation. Expression of melanoma antigen-1 (MAGE-1), synovial sarcoma X breakpoint-1 (SSX-1), and cancer-testis-associated protein of 11 kDa (CTp11) mRNA in peripheral blood mononuclear cells (PBMC) was tested by nested reverse transcripts-polymerase chain reaction (RT-PCR). Serum α-fetoprotein (AFP) in these patients was also determined.
RESULTS: The positive rate of MAGE-1, SSX-1 and CTp11 transcripts was 37.7%, 34.4%, 31.1% in PBMC samples, and 74.4%, 73.3%, 62.2% in their resected tumor samples, respectively. The positive rate for at least one of the transcripts of three CTA genes was 66.7% in PBMC samples and 91.1% in their resected tumor samples. MAGE-1, SSX-1 and/or CTp11 mRNA were not detected in the PBMC of those patients from whom the resected tumor samples were MAGE-1, SSX-1 and/or CTp11 mRNA negative, nor in the PBMC samples from 20 healthy donors and 10 cirrhotic patients. Among the 90 patients, the serum AFP in 44 patients met the general diagnostic standard (AFP > 400 μg/L) for HCC, and was negative (AFP ≤ 20 μg/L) or positive with a low concentration (20 μg/L < AFP ≤ 400 μg/L) in the other patients. The positive rate for at least one of the transcripts of three CTA genes in PBMC samples from the AFP negative or positive patients with a low concentration was 69.2% and 45.0%, respectively. Of the 90 patients, 71 (78.9%) were diagnosed as HCC by nested RT-PCR and serum AFP. Although the positive rate for at least one of the transcripts of three CTA genes in PBMC samples from 53 patients at TNM stage III or IV was obviously higher than that in PBMC samples from 37 patients at stage I or II (77.9% vs 51.4%, P = 0.010), the CTA mRNA was detected in 41.7% and 56.0% of PBMC samples from HCC patients at stages I and II, respectively.
CONCLUSION: Detecting MAGE-1, SSX-1 and CTp11 mRNA in PBMC improves the total diagnostic rate of HCC.
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Zhao L, Mou DC, Peng JR, Leng XS. Expression of cancer-testis antigen SPANX-C mRNA in human hepatocellular carcinoma and prediction of HLA-A2-restricted CTL epitopes of SPANX-C. Shijie Huaren Xiaohua Zazhi 2010; 18:1810-1814. [DOI: 10.11569/wcjd.v18.i17.1810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of SPANX-C (sperm protein associated with the nucleus mapped to the X chromosome-C) gene in hepatocellular carcinoma (HCC) and to predict the HLA-A2-restricted cytotoxic T lymphocyte (CTL) epitopes of SPANX-C to find new targets for specific immunotherapy of HCC.
METHODS: The expression of SPANX-C mRNA was characterized by RT-PCR in tumor tissue and adjacent liver tissue specimens from 115 HCC patients and liver tissue specimens from 20 non-HCC patients (10 with liver cirrhosis and 10 without liver disease). The positive PCR products (297 bp) obtained from 5 tumor tissue specimens were randomly selected for sequencing to confirm the detecting results. HLA-A2-restricted CTL epitopes of SPANX-C were predicted by peptide supermotif prediction method in combination with quantitative motif method.
RESULTS: Seventy (60.9%) of 115 tumor tissue specimen from HCC patients expressed SPANX-C mRNA. In contrast, SPANX-C mRNA was not detected in tumor-adjacent tissue and liver tissue from non-HCC patients. There was no discernable correlation between SPANX-C expression and tumor stage, differentiation degree or serum α-fetoprotein level (all P > 0.05). Five CTL epitope candidates (nonamers) derived from the antigen SPANX-C were found by peptide supermotif prediction, of them, SPANX-C51-59 (LVVRYRRNV) may have stronger binding potential with HLA-A2 molecule.
CONCLUSION: SPANX-C mRNA is highly expressed in HCC tumor tissue in Chinese patients. SPANX-C may provide potential HLA-A2-restricted CTL epitopes as specific targets for immunotherapy of HCC.
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