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Yabushita T, Shimomura Y, Maruoka H, Katoh D, Yamashita D, Satake H, Hiramoto N, Yoshioka S, Yonetani N, Nishikori M, Morimoto T, Imai Y, Ishikawa T. Complete detection of FR1 to FR3 primer-based PCR patterns of immunoglobulin heavy chain rearrangement in the BIOMED-2 protocol is associated with poor prognosis in patients with diffuse large B-cell lymphoma. EJHAEM 2024; 5:698-708. [PMID: 39157631 PMCID: PMC11327714 DOI: 10.1002/jha2.921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 08/20/2024]
Abstract
Somatic hypermutations (SHMs) in the variable region (VH) of the immunoglobulin heavy chain (IgH) gene are common in diffuse large B-cell lymphoma (DLBCL). Recently, IgH VH SHMs have become known as immunogenic neoantigens, but few studies have evaluated the prognostic impact of the frequency of VH SHMs in DLBCL. The BIOMED-2 protocol is the gold standard polymerase chain reaction (PCR) for clonality analysis in lymphoid malignancies, but can produce false negatives due to the presence of IgH VH SHMs. To overcome this problem, three primer sets were designed for the three framework regions (FR1, FR2, and FR3). We evaluated the predictive value of this PCR pattern in patients with DLBCL. To evaluate the prognostic impact of complete detection of the clonal amplifications (VHFR1-JH, VHFR2-JH, and VHFR3-JH) in the BIOMED-2 protocol, we retrospectively analyzed 301 DLBCL patients who were initially treated with anthracycline-based immunochemotherapy. Complete detection of the FR1 to FR3 primer-based IgH VH PCR patterns in the BIOMED-2 protocol was associated with low frequency of VH SHMs (p < 0.001). Patients who were positive for all these three PCRs (n = 79) were significantly associated with shorter 5-year overall survival (OS; 54.2% vs. 73.2%; p = 0.002) and progression-free survival (PFS; 34.3% vs. 59.3%; p < 0.001) compared to patients with other PCR patterns (n = 202). Specifically, the successful FR3-JH detection was associated with significantly worse OS (p < 0.001) and PFS (p < 0.001). PCR patterns of complete IgH rearrangement using the BIOMED-2 protocol are clinically meaningful indicators for prognostic stratification of DLBCL patients.
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Affiliation(s)
- Tomohiro Yabushita
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
- International Research Center for Medical SciencesKumamoto UniversityKumamotoJapan
| | | | - Hayato Maruoka
- Department of Clinical LaboratoryKobe City Medical Center General HospitalKobeJapan
| | - Daisuke Katoh
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
| | - Daisuke Yamashita
- Department of PathologyKobe City Medical Center General HospitalKobeJapan
| | - Hironaga Satake
- Department of Medical OncologyKobe City Medical Center General HospitalKobeJapan
- Department of Medical OncologyKochi Medical SchoolKochiJapan
| | - Nobuhiro Hiramoto
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
| | - Satoshi Yoshioka
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
- Department of HematologyJapanese Red Cross Osaka HospitalOsakaJapan
| | - Noboru Yonetani
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
| | - Momoko Nishikori
- Department of Hematology and Oncology, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Takeshi Morimoto
- Clinical Research CenterKobe City Medical Center General HospitalKobeJapan
- Department of Clinical EpidemiologyHyogo College of MedicineHyogoJapan
| | - Yukihiro Imai
- Department of PathologyKobe City Medical Center General HospitalKobeJapan
- Department of Surgical PathologyKakogawa Central City HospitalKakogawaJapan
| | - Takayuki Ishikawa
- Department of HematologyKobe City Medical Center General HospitalKobeJapan
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Tan KT, Ding LW, Sun QY, Lao ZT, Chien W, Ren X, Xiao JF, Loh XY, Xu L, Lill M, Mayakonda A, Lin DC, Yang H, Koeffler HP. Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines. BMC Cancer 2018; 18:940. [PMID: 30285677 PMCID: PMC6167786 DOI: 10.1186/s12885-018-4840-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 09/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clonal VDJ rearrangement of B/T cell receptors (B/TCRs) occurring during B/T lymphocyte development has been used as a marker to track the clonality of B/T cell populations. METHODS We systematically profiled the B/T cell receptor repertoire of 936 cancer cell lines across a variety of cancer types as well as 462 Epstein-Barr Virus (EBV) transformed normal B lymphocyte lines using RNA sequencing data. RESULTS Rearranged B/TCRs were readily detected in cell lines derived from lymphocytes, and subclonality or potential biclonality were found in a number of blood cancer cell lines. Clonal BCR/TCR rearrangements were detected in several blast phase CML lines and unexpectedly, one gastric cancer cell line (KE-97), reflecting a lymphoid origin of these cells. Notably, clonality was highly prevalent in EBV transformed B lymphocytes, suggesting either transformation only occurred in a few B cells or those with a growth advantage dominated the transformed population through clonal evolution. CONCLUSIONS Our analysis reveals the complexity and heterogeneity of the BCR/TCR rearrangement repertoire and provides a unique insight into the clonality of lymphocyte derived cell lines.
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Affiliation(s)
- Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Zhen-Tang Lao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Wenwen Chien
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xin Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Michael Lill
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
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DiNapoli SR, Ortiz AM, Wu F, Matsuda K, Twigg HL, Hirsch VM, Knox K, Brenchley JM. Tissue-resident macrophages can contain replication-competent virus in antiretroviral-naive, SIV-infected Asian macaques. JCI Insight 2017; 2:e91214. [PMID: 28239657 DOI: 10.1172/jci.insight.91214] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
SIV DNA can be detected in lymphoid tissue-resident macrophages of chronically SIV-infected Asian macaques. These macrophages also contain evidence of recently phagocytosed SIV-infected CD4+ T cells. Here, we examine whether these macrophages contain replication-competent virus, whether viral DNA can be detected in tissue-resident macrophages from antiretroviral (ARV) therapy-treated animals and humans, and how the viral sequences amplified from macrophages and contemporaneous CD4+ T cells compare. In ARV-naive animals, we find that lymphoid tissue-resident macrophages contain replication-competent virus if they also contain viral DNA in ARV-naive Asian macaques. The genetic sequence of the virus within these macrophages is similar to those within CD4+ T cells from the same anatomic sites. In ARV-treated animals, we find that viral DNA can be amplified from lymphoid tissue-resident macrophages of SIV-infected Asian macaques that were treated with ARVs for at least 5 months, but we could not detect replication-competent virus from macrophages of animals treated with ARVs. Finally, we could not detect viral DNA in alveolar macrophages from HIV-infected individuals who received ARVs for 3 years and had undetectable viral loads. These data demonstrate that macrophages can contain replication-competent virus, but may not represent a significant reservoir for HIV in vivo.
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Affiliation(s)
| | | | - Fan Wu
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Kenta Matsuda
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Vanessa M Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Kenneth Knox
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
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Calantone N, Wu F, Klase Z, Deleage C, Perkins M, Matsuda K, Thompson EA, Ortiz AM, Vinton CL, Ourmanov I, Loré K, Douek DC, Estes JD, Hirsch VM, Brenchley JM. Tissue myeloid cells in SIV-infected primates acquire viral DNA through phagocytosis of infected T cells. Immunity 2014; 41:493-502. [PMID: 25238099 DOI: 10.1016/j.immuni.2014.08.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
The viral accessory protein Vpx, expressed by certain simian and human immunodeficiency viruses (SIVs and HIVs), is thought to improve viral infectivity of myeloid cells. We infected 35 Asian macaques and African green monkeys with viruses that do or do not express Vpx and examined viral targeting of cells in vivo. While lack of Vpx expression affected viral dynamics in vivo, with decreased viral loads and infection of CD4⁺ T cells, Vpx expression had no detectable effect on infectivity of myeloid cells. Moreover, viral DNA was observed only within myeloid cells in tissues not massively depleted of CD4⁺ T cells. Myeloid cells containing viral DNA also showed evidence of T cell phagocytosis in vivo, suggesting that their viral DNA may be attributed to phagocytosis of SIV-infected T cells. These data suggest that myeloid cells are not a major source of SIV in vivo, irrespective of Vpx expression.
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Affiliation(s)
- Nina Calantone
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Fan Wu
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Zachary Klase
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Molly Perkins
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Kenta Matsuda
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Elizabeth A Thompson
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Department of Medicine, Karolinska Institutet, Stockholm 171, Sweden
| | | | - Carol L Vinton
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ilnour Ourmanov
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Karin Loré
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Department of Medicine, Karolinska Institutet, Stockholm 171, Sweden
| | - Daniel C Douek
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Vanessa M Hirsch
- Lab of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
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