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Jindal K, Adil MT, Yamaguchi N, Yang X, Wang HC, Kamimoto K, Rivera-Gonzalez GC, Morris SA. Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes. Nat Biotechnol 2024; 42:946-959. [PMID: 37749269 PMCID: PMC11180607 DOI: 10.1038/s41587-023-01931-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Complex gene regulatory mechanisms underlie differentiation and reprogramming. Contemporary single-cell lineage-tracing (scLT) methods use expressed, heritable DNA barcodes to combine cell lineage readout with single-cell transcriptomics. However, reliance on transcriptional profiling limits adaptation to other single-cell assays. With CellTag-multi, we present an approach that enables direct capture of heritable random barcodes expressed as polyadenylated transcripts, in both single-cell RNA sequencing and single-cell Assay for Transposase Accessible Chromatin using sequencing assays, allowing for independent clonal tracking of transcriptional and epigenomic cell states. We validate CellTag-multi to characterize progenitor cell lineage priming during mouse hematopoiesis. Additionally, in direct reprogramming of fibroblasts to endoderm progenitors, we identify core regulatory programs underlying on-target and off-target fates. Furthermore, we reveal the transcription factor Zfp281 as a regulator of reprogramming outcome, biasing cells toward an off-target mesenchymal fate. Our results establish CellTag-multi as a lineage-tracing method compatible with multiple single-cell modalities and demonstrate its utility in revealing fate-specifying gene regulatory changes across diverse paradigms of differentiation and reprogramming.
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Affiliation(s)
- Kunal Jindal
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mohd Tayyab Adil
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Naoto Yamaguchi
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xue Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Helen C Wang
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Guillermo C Rivera-Gonzalez
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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2
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Wu Y, Wang V, Yarchoan R. Pacritinib inhibits proliferation of primary effusion lymphoma cells and production of viral interleukin-6 induced cytokines. Sci Rep 2024; 14:4125. [PMID: 38374336 PMCID: PMC10876599 DOI: 10.1038/s41598-024-54453-7] [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: 08/25/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
Primary effusion lymphoma (PEL) and a form of multicentric Castleman's disease (MCD) are both caused by Kaposi sarcoma herpesvirus (KSHV). There is a critical need for improved therapies for these disorders. The IL-6/JAK/STAT3 pathway plays an important role in the pathogenesis of both PEL and KSHV-MCD. We explored the potential of JAK inhibitors for use in PEL and KSHV-MCD, and found that pacritinib was superior to others in inhibiting the growth of PEL cell lines. Pacritinib induced apoptosis in PEL cells and inhibited STAT3 and NF-κB activity as evidenced by reduced amount of phosphorylated moieties. Pacritinib also inhibits FLT3, IRAK1, and ROS1; studies utilizing other inhibitors of these targets revealed that only FLT3 inhibitors exhibited similar cell growth inhibitory effects. FLT3's likely contribution to pacritinib's cell growth inhibition was further demonstrated by siRNA knockdown of FLT3. RNA sequencing and RT-PCR showed that many key host genes including cyclins and IL-6 were downregulated by pacritinib, while KSHV genes were variably altered. Finally, pacritinib suppressed KSHV viral IL-6-induced human IL-6 and IL-10 production in peripheral blood mononuclear cells, which may model an important step in KSHV-MCD pathogenesis. These results suggest that pacritinib warrants testing for the treatment of KSHV-MCD and PEL.
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Affiliation(s)
- Yiquan Wu
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Building 10, Rm. 6N106, MSC 1868, Bethesda, MD, 20892-1868, USA
| | - Victoria Wang
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Building 10, Rm. 6N106, MSC 1868, Bethesda, MD, 20892-1868, USA
| | - Robert Yarchoan
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, 10 Center Drive, Building 10, Rm. 6N106, MSC 1868, Bethesda, MD, 20892-1868, USA.
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3
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Kovach AE, Wood BL. Updates on lymphoblastic leukemia/lymphoma classification and minimal/measurable residual disease analysis. Semin Diagn Pathol 2023; 40:457-471. [PMID: 37953192 DOI: 10.1053/j.semdp.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Lymphoblastic leukemia/lymphoma (ALL/LBL), especially certain subtypes, continues to confer morbidity and mortality despite significant therapeutic advances. The pathologic classification of ALL/LBL, especially that of B-ALL, has recently substantially expanded with the identification of several distinct and prognostically important genetic drivers. These discoveries are reflected in both current classification systems, the World Health Organization (WHO) 5th edition and the new International Consensus Classification (ICC). In this article, novel subtypes of B-ALL are reviewed, including DUX4, MEF2D and ZNF384-rearranged B-ALL; the rare pediatric entity B-ALL with TLF3::HLF, now added to the classifications, is discussed; updates to the category of B-ALL with BCR::ABL1-like features (Ph-like B-ALL) are summarized; and emerging genetic subtypes of T-ALL are presented. The second half of the article details current approaches to minimal/measurable residual disease (MRD) detection in B-ALL and T-ALL and presents anticipated challenges to current approaches in the burgeoning era of antigen-directed immunotherapy.
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Affiliation(s)
- Alexandra E Kovach
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
| | - Brent L Wood
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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4
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Korzhenevich J, Janowska I, van der Burg M, Rizzi M. Human and mouse early B cell development: So similar but so different. Immunol Lett 2023; 261:1-12. [PMID: 37442242 DOI: 10.1016/j.imlet.2023.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/09/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Early B cell development in the bone marrow ensures the replenishment of the peripheral B cell pool. Immature B cells continuously develop from hematopoietic stem cells, in a process guided by an intricate network of transcription factors as well as chemokine and cytokine signals. Humans and mice possess somewhat similar regulatory mechanisms of B lymphopoiesis. The continuous discovery of monogenetic defects that impact early B cell development in humans substantiates the similarities and differences with B cell development in mice. These differences become relevant when targeted therapeutic approaches are used in patients; therefore, predicting potential immunological adverse events is crucial. In this review, we have provided a phenotypical classification of human and murine early progenitors and B cell stages, based on surface and intracellular protein expression. Further, we have critically compared the role of key transcription factors (Ikaros, E2A, EBF1, PAX5, and Aiolos) and chemo- or cytokine signals (FLT3, c-kit, IL-7R, and CXCR4) during homeostatic and aberrant B lymphopoiesis in both humans and mice.
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Affiliation(s)
- Jakov Korzhenevich
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Iga Janowska
- Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany
| | - Mirjam van der Burg
- Department of Pediatrics, Laboratory for Pediatric Immunology, Willem-Alexander Children's Hospital, Leiden University Medical Center, 2333, ZA Leiden, The Netherlands
| | - Marta Rizzi
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria; Department of Rheumatology and Clinical Immunology, Freiburg University Medical Center, University of Freiburg, 79106, Freiburg, Germany; Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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5
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Zhang B, Zhao D, Chen F, Frankhouser D, Wang H, Pathak KV, Dong L, Torres A, Garcia-Mansfield K, Zhang Y, Hoang DH, Chen MH, Tao S, Cho H, Liang Y, Perrotti D, Branciamore S, Rockne R, Wu X, Ghoda L, Li L, Jin J, Chen J, Yu J, Caligiuri MA, Kuo YH, Boldin M, Su R, Swiderski P, Kortylewski M, Pirrotte P, Nguyen LXT, Marcucci G. Acquired miR-142 deficit in leukemic stem cells suffices to drive chronic myeloid leukemia into blast crisis. Nat Commun 2023; 14:5325. [PMID: 37658085 PMCID: PMC10474062 DOI: 10.1038/s41467-023-41167-z] [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: 11/07/2022] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
The mechanisms underlying the transformation of chronic myeloid leukemia (CML) from chronic phase (CP) to blast crisis (BC) are not fully elucidated. Here, we show lower levels of miR-142 in CD34+CD38- blasts from BC CML patients than in those from CP CML patients, suggesting that miR-142 deficit is implicated in BC evolution. Thus, we create miR-142 knockout CML (i.e., miR-142-/-BCR-ABL) mice, which develop BC and die sooner than miR-142 wt CML (i.e., miR-142+/+BCR-ABL) mice, which instead remain in CP CML. Leukemic stem cells (LSCs) from miR-142-/-BCR-ABL mice recapitulate the BC phenotype in congenic recipients, supporting LSC transformation by miR-142 deficit. State-transition and mutual information analyses of "bulk" and single cell RNA-seq data, metabolomic profiling and functional metabolic assays identify enhanced fatty acid β-oxidation, oxidative phosphorylation and mitochondrial fusion in LSCs as key steps in miR-142-driven BC evolution. A synthetic CpG-miR-142 mimic oligodeoxynucleotide rescues the BC phenotype in miR-142-/-BCR-ABL mice and patient-derived xenografts.
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Affiliation(s)
- Bin Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
| | - Dandan Zhao
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Fang Chen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - David Frankhouser
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Huafeng Wang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Khyatiben V Pathak
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Anakaren Torres
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Krystine Garcia-Mansfield
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Yi Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Dinh Hoa Hoang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Min-Hsuan Chen
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Shu Tao
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Hyejin Cho
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Yong Liang
- DNA/RNA Peptide Shared Resources, Beckman Research Institute, Duarte, CA, USA
| | - Danilo Perrotti
- Department of Medicine and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine Baltimore, Baltimore, MD, USA
- Department of Immunology and Inflammation, Centre of Hematology, Imperial College of London, London, UK
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Russell Rockne
- Department of Computational and Quantitative Medicine, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Xiwei Wu
- City of Hope National Medical Center, Integrative Genomics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute, Duarte, CA, USA
| | - Lucy Ghoda
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Jie Jin
- Department of Hematology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Michael A Caligiuri
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA
| | - Mark Boldin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Piotr Swiderski
- DNA/RNA Peptide Shared Resources, Beckman Research Institute, Duarte, CA, USA
| | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, Duarte, CA, USA
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Le Xuan Truong Nguyen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope Medical Center and Beckman Research Institute, Duarte, CA, USA.
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6
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The Pleiotropy of PAX5 Gene Products and Function. Int J Mol Sci 2022; 23:ijms231710095. [PMID: 36077495 PMCID: PMC9456430 DOI: 10.3390/ijms231710095] [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: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
PAX5, a member of the Paired Box (PAX) transcription factor family, is an essential factor for B-lineage identity during lymphoid differentiation. Mechanistically, PAX5 controls gene expression profiles, which are pivotal to cellular processes such as viability, proliferation, and differentiation. Given its crucial function in B-cell development, PAX5 aberrant expression also correlates with hallmark cancer processes leading to hematological and other types of cancer lesions. Despite the well-established association of PAX5 in the development, maintenance, and progression of cancer disease, the use of PAX5 as a cancer biomarker or therapeutic target has yet to be implemented. This may be partly due to the assortment of PAX5 expressed products, which layers the complexity of their function and role in various regulatory networks and biological processes. In this review, we provide an overview of the reported data describing PAX5 products, their regulation, and function in cellular processes, cellular biology, and neoplasm.
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7
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Flt3 Signaling in B Lymphocyte Development and Humoral Immunity. Int J Mol Sci 2022; 23:ijms23137289. [PMID: 35806293 PMCID: PMC9267047 DOI: 10.3390/ijms23137289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
The Class III receptor tyrosine kinase Flt3 and its ligand, the Flt3-ligand (FL), play an integral role in regulating the proliferation, differentiation, and survival of multipotent hematopoietic and lymphoid progenitors from which B cell precursors derive in bone marrow (BM). More recently, essential roles for Flt3 signaling in the regulation of peripheral B cell development and affinity maturation have come to light. Experimental findings derived from a multitude of mouse models have reinforced the importance of molecular and cellular regulation of Flt3 and FL in lymphohematopoiesis and adaptive immunity. Here, we provide a comprehensive review of the current state of the knowledge regarding molecular and cellular regulation of Flt3/FL and the roles of Flt3 signaling in hematopoietic stem cell (HSC) activation, lymphoid development, BM B lymphopoiesis, and peripheral B cell development. Cumulatively, the literature has reinforced the importance of Flt3 signaling in B cell development and function. However, it has also identified gaps in the knowledge regarding Flt3-dependent developmental-stage specific gene regulatory circuits essential for steady-state B lymphopoiesis that will be the focus of future studies.
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Concurrent CDX2 cis-deregulation and UBTF-ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL. Blood 2022; 139:3505-3518. [PMID: 35316324 PMCID: PMC9203705 DOI: 10.1182/blood.2021014723] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/12/2022] [Indexed: 11/20/2022] Open
Abstract
CDX2 cis-deregulation and UBTF::ATXN7L3 fusion driven by focal deletions define a novel subtype of B-ALL. CDX2/UBTF::ATXN7L3 is a high-risk B-ALL subtype in young adults, which warrants improved therapeutic strategies.
Oncogenic alterations underlying B-cell acute lymphoblastic leukemia (B-ALL) in adults remain incompletely elucidated. To uncover novel oncogenic drivers, we performed RNA sequencing and whole-genome analyses in a large cohort of unresolved B-ALL. We identified a novel subtype characterized by a distinct gene expression signature and the unique association of 2 genomic microdeletions. The 17q21.31 microdeletion resulted in a UBTF::ATXN7L3 fusion transcript encoding a chimeric protein. The 13q12.2 deletion resulted in monoallelic ectopic expression of the homeobox transcription factor CDX2, located 138 kb in cis from the deletion. Using 4C-sequencing and CRISPR interference experiments, we elucidated the mechanism of CDX2 cis-deregulation, involving PAN3 enhancer hijacking. CDX2/UBTF ALL (n = 26) harbored a distinct pattern of additional alterations including 1q gain and CXCR4 activating mutations. Within adult patients with Ph− B-ALL enrolled in GRAALL trials, patients with CDX2/UBTF ALL (n = 17/723, 2.4%) were young (median age, 31 years) and dramatically enriched in females (male/female ratio, 0.2, P = .002). They commonly presented with a pro-B phenotype ALL and moderate blast cell infiltration. They had poor response to treatment including a higher risk of failure to first induction course (19% vs 3%, P = .017) and higher post-induction minimal residual disease (MRD) levels (MRD ≥ 10−4, 93% vs 46%, P < .001). This early resistance to treatment translated into a significantly higher cumulative incidence of relapse (75.0% vs 32.4%, P = .004) in univariate and multivariate analyses. In conclusion, we discovered a novel B-ALL entity defined by the unique combination of CDX2 cis-deregulation and UBTF::ATXN7L3 fusion, representing a high-risk disease in young adults.
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9
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FLT3 mutational analysis in acute myeloid leukemia: Advantages and pitfalls with different approaches. Blood Rev 2022; 54:100928. [DOI: 10.1016/j.blre.2022.100928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/17/2022]
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10
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Ruiz-Ordoñez I, Piedrahita JM, Arévalo JA, Agualimpia A, Tobón GJ. Lymphomagenesis predictors and related pathogenesis. J Transl Autoimmun 2021; 4:100098. [PMID: 33889831 PMCID: PMC8050773 DOI: 10.1016/j.jtauto.2021.100098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Sjögren's syndrome (SS) is a systemic autoimmune disease characterised by a wide range of clinical manifestations and complications, including B-cell lymphoma. This study aims to describe the predictors associated with lymphomagenesis in patients with Sjögren's syndrome, emphasising the pathophysiological bases that support this association. We performed a review of the literature published through a comprehensive search strategy in PubMed/MEDLINE, Scopus, and Web of science. Forty publications describing a total of 45,208 patients with SS were retrieved. The predictors were grouped according to their pathophysiological role in the lymphoproliferation process. Also, some new biomarkers such as MicroRNAs, P2X7 receptor-NLRP3 inflammasome, Thymic stromal lymphopoietin, and Three-prime repair exonuclease 1 (TREX1) were identified. The knowledge of the pathophysiology allows the discrimination of markers that participate in the initial stages. Considering that the lymphoproliferation process includes the progression of lymphoma towards more aggressive subtypes, it is essential to recognise biomarkers associated with a worse prognosis.
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Affiliation(s)
- Ingrid Ruiz-Ordoñez
- Fundación Valle del Lili, Centro de Investigaciones Clínicas, Cra 98 No. 18-49, Cali, 760032, Colombia
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
| | - Juan-Manuel Piedrahita
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
| | - Javier-Andrés Arévalo
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Universidad Icesi, Calle 18 No. 122-135, Cali, Colombia
| | - Andrés Agualimpia
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Fundación Valle del Lili, Unidad de Reumatología, Cra 98 No. 18-49, Cali. 760032, Colombia
| | - Gabriel J Tobón
- Universidad Icesi, Centro de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional, Cali, Colombia
- Fundación Valle del Lili, Unidad de Reumatología, Cra 98 No. 18-49, Cali. 760032, Colombia
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11
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Khalid A, Aslam S, Ahmed M, Hasnain S, Aslam A. Risk assessment of FLT3 and PAX5 variants in B-acute lymphoblastic leukemia: a case-control study in a Pakistani cohort. PeerJ 2019; 7:e7195. [PMID: 31565544 PMCID: PMC6743442 DOI: 10.7717/peerj.7195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/28/2019] [Indexed: 11/20/2022] Open
Abstract
AIMS B-cell acute lymphoblastic leukemia (B-ALL) is amongst the most prevalent cancers of children in Pakistan. Genetic variations in FLT3 are associated with auto-phosphorylation of kinase domain that leads to increased proliferation of blast cells. Paired box family of transcription factor (PAX5) plays a critical role in commitment and differentiation of B-cells. Variations in PAX5 are associated with the risk of B-ALL. We aimed to analyze the association of FLT3 and PAX5 polymorphisms with B cell leukemia in Pakistani cohort. METHODS We collected 155 B-ALL subject and 155 control blood samples. For analysis, genotyping was done by tetra ARMS-PCR. SPSS was used to check the association of demographic factors of SNPs present in the population with the risk of B-ALL. RESULTS Risk allele frequency A at locus 13q12.2 (rs35958982, FLT3) was conspicuous and showed positive association (OR = 2.30, CI [1.20–4.50], P = 0.005) but genotype frequency (OR = 3.67, CI [0.75–18.10], P = 0.088) failed to show any association with the disease. At locus 9p13.2 (rs3780135, PAX5), the risk allele frequency was significantly higher in B-ALL subjects than ancestral allele frequency (OR = 2.17, CI [1.37–3.43], P = 0.000). Genotype frequency analysis of rs3780135 polymorphism exhibited the protective effect (OR = 0.55, CI [0.72–1.83], P = 0.029). At locus 13q12.2 (rs12430881, FLT3), the minor allele frequency G (OR = 1.15, CI [1.37–3.43], P = 0.043) and genotype frequency (OR = 2.52, P = 0.006) reached significance as showed p < 0.05. CONCLUSION In the present study, a strong risk of B-cell acute lymphoblastic leukemia was associated with rs35958982 and rs12430881 polymorphisms. However, rs3780135 polymorphism showed the protective effect. Additionally, other demographic factors like family history, smoking and consanguinity were also found to be important in risk assessment. We anticipate that the information from genetic variations in this study can aid in therapeutic approach in the future.
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Affiliation(s)
- Ammara Khalid
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Sara Aslam
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Mehboob Ahmed
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Shahida Hasnain
- Department of Microbiology & Molecular Genetics, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
| | - Aimen Aslam
- Department of Statistics and Actuarial Science, Quaid-e-Azam Campus, University of the Punjab, Lahore, Pakistan
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