Summary of single-cell genomics studies in immune BMF
| Disease . | Content . | Method . | Platform . | Sample . | Patient cohort . | Disease pathogenesis . | Treatment . | Key finding . | Reference . |
|---|---|---|---|---|---|---|---|---|---|
| AA | T-cell landscape of immune AA | TCRβ-seq and scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | T cells from BM and PB | 153 patients with AA (samples at diagnosis, during remission, and at relapse) | Yes | Yes | Private clonotypes in patients with immune AA may recognize a common antigen; AA signature clonotypes were of effector phenotypes and fluctuate after IST. | 64 |
| AA | Somatic mutations in lymphocytes in immune AA, and phenotypes of STAT3-mutated clones | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Purified T-cell clones | Serial samples from 2 index patients with SAA | Yes | Yes | Somatic mutations were common in patients with AA, enriched in CD8+ T cells, and accumulated most on the JAK-STAT and MAPK pathways; a STAT3-mutated clone was cytotoxic and attenuated by successful IST. | 65 |
| AA | Immune cell phenotypes in pediatric SAA | Single-cell mass cytometry and scRNA-seq | CyTOF and chromium system, 5′ (10x Genomics) | BMMNCs | Nine at diagnosis, 3 after IST, and 4 healthy donors | Yes | Yes | Th17-polarized CD4+ naive T cells with the JAK3/STAT3 pathway activation in pediatric SAA. | 66 |
| AA | Multiomics analysis of AA and a murine model | Publicly available scRNA-seq data (GSE145669) from references, microarray data (GSE3807), and liquid chromatography/mass spectrometry | N/A | Plasma for proteomics; BM-derived HSPCs, CD4+ and CD8+ T cells from the BM and PB (scRNA-seq data from reference 28); and sorted CD3+ T cells (microarray data from GSE3807) | Plasma from 14 patients with SAA and 15 healthy donors | Yes | N/A | Differential proteomics and metabolomics in AA, a population of activated CD8+CD38+ T cells involved in AA. | 67 |
| AA | Single-cell transcriptome of hematopoietic cells and T cells | Full-length scRNA-seq | STRT-seq and full-length Smart-seq2 | BM-derived HSPCs and CD4+ and CD8+ T cells from the BM and PB | Fifteen patients with treatment-naïve AA, including 12 with non-SAA, 3 with SAA, and 4 healthy donors; 5 patients with non-SAA responsive to cyclosporine A plus androgens treatment | Yes | Yes | Selective lineage disruption, alternative splicing, and polyadenylation in AA; cell type–specific ligand–receptor interactions. | 68 |
| AA | NK cell phenotypes in SAA | scRNA-seq | Chromium system, 3′ (10x Genomics) | Sorted NK cells from the BM and PB | Three patients with treatment-naive SAA | Yes | N/A | NK cell subsets altered in SAA. | 70 |
| AA | Single-cell transcriptome of BM cells | scRNA-seq | Chromium system, 3′ (10x Genomics) | BMMNCs and enriched CD34+ cells | Two patients with SAA and 2 healthy donors | Yes | N/A | Dysregulated gene expression of hematopoietic cells, and altered BCR usage and interactions with other cell types. | 77 |
| MDS and CH | Impact of splicing aberrations in human hematopoiesis | Single-cell multiomics: surface protein, gene expression, and RNA splicing | GoT-Splice | CD34+ cells | Six patients with MDS and 2 with CH | Yes | N/A | SF3B1 mutations altered 3' splicing site usage and lineage output in MDS and CH. | 85 |
| MDS | Hematopoietic differentiation and monosomy 7 cells in MDS | scRNA-seq | C1 Fluidigm | Lin−CD34+CD38+ and Lin−CD34+CD38− cells | Five patients with MDS (3 evolved from AA) and 4 healthy donors | Yes | Yes | Distinct differentiation patterns of patients with MDS, and differential gene programs in monosomy 7 cells compared with diploid cells. | 93 |
| MDS | lncRNA landscape in human HSPCs | scRNA-seq | C1 Fluidigm | Lin−CD34+CD38+ and Lin−CD34+CD38− cells | Five patients with MDS (3 evolved from AA) and 4 healthy donors | Yes | Yes | lncRNAs in HSPCs were stage- and cell-type specific, and closely correlated with protein-coding genes in the regulation of hematopoiesis and cell fate decisions; there was differential lncRNA expression in MDS and aneuploid cells. | 94 |
| MDS | HSPCs | scRNA-seq | Chromium system, 3′ (10x Genomics) | Lin− cells from the BM | Five patients with MDS, 2 with secondary AML, and 17 healthy donors (from GSE120221) | Yes | N/A | Abnormal proliferation, RNA metabolism, and ribosome biogenesis in MDS stem cells. | 80 |
| MDS | Stem cell architecture and association with disease progression and response to therapy in MDS | scRNA-seq | Chromium system, 3′ (10x Genomics) | Lin−CD34+ HSPCs | One patient with MDS with a GMP pattern and 1 patient with MDS with a CMP pattern | Yes | Yes | scRNA-seq to validate the distinct differentiation pattern in patients with MDS, and this stem cell architecture was associated with disease progression and response to therapy. | 81 |
| MDS | Frequency and basis for coexistence of splicing factor mutations | scDNA-seq | Mission Bio | BMMNCs | Eleven patients with myeloid neoplasm and double splicing factor mutations | Yes | N/A | Escape from epistasis of RNA splicing factor mutations occured with specific mutation alleles and preservation of 1 wild-type allele. | 86 |
| MDS | Somatic mutations and copy number variations during disease progression and treatment resistance | scDNA-seq | Tapestri Single-cell DNA AML Panel Kit | BM samples | Serial samples of 2 patients with MDS treated with HMA | Yes | Yes | Disease progression and resistance to HMA was accompanied by changes in clone heterogeneity of pathogenic mutations and acquisition of copy number variations. | 87 |
| T-LGLL | T-cell clonotypes and phenotypes in T-LGLL | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Enriched CD45+ cells from PBMCs | Nine patients with T-LGLL and 6 healthy controls | Yes | N/A | T-LGLL clonotypes were more cytotoxic and exhausted than healthy reactive clonotypes; nonleukemic T cell repertoire was also more mature, cytotoxic, and clonally restricted than in other cancers and autoimmune disorders; and leukemic T-LGLL clonotypes shared TCR similarities with their nonleukemic repertoires. | 96 |
| T-LGLL | T-cell clonotypes and phenotypes in T-LGLL and with treatment | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Enriched CD3+ T cells from PBMCs | Thirteen patients with T-LGLL (12 had paired samples before and 3 or 6 mo after alemtuzumab treatment) and 6 healthy controls | Yes | Yes | There was a lack of common clonotypes of TCR usage in T-LGLL; dysregulated cell survival programs featured with downregulation of apoptosis genes were prominent in T-LGLL cells; apoptosis genes were upregulated after alemtuzumab treatment, more in responders than in nonresponders; and TCR diversity was further skewed after treatment. | 97 |
| CH | Impact of DNMT3A and TET2 mutations on hematopoietic differentiation | Multiomic single-cell analysis: index sorting, scRNA-seq, and genotyping | Target-seq+ | BM samples | Nine CH samples with predicted loss-of-function mutations | Yes | N/A | DNMT3A-mutant and TET2-mutant clones expand in a different manner; and there was a non–cell autonomous impact on WT HSCs in CH. | 98 |
| CH | DNMT3A R882 mutations on hematopoiesis | Multiomic single-cell analysis: capturing genotype, transcriptomes, and methylomes | GoT | CD34+ HSPCs | Three patients with multiple myeloma and DNMT3A R882 mutations | Yes | N/A | DNMT3A R882 mutations perturbed early progenitor states through selective hypomethylation. | 99 |
| CH | Pathogenesis of CH | Simultaneous detection of gene mutations and expression on single cells | Fluidigm C1-HT system | BM-derived HSPCs | Sixteen patients with CH and 16 healthy controls | Yes | N/A | There were non–cell-autonomous phenotypes or an altered BM environment that favored the positive selection of CH− clones. | 100 |
| BMF | Cellular and molecular features associated with CAR T-associated prolonged cytopenia | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | BM samples | Sixteen patients with DLBCL who had prolonged cytopenia after treatment with axi-cel | Yes | Yes | Clonally expanded IFN-γ–expressing cytotoxic T cells and an enrichment of IFN signaling within the HSCs of BM aspirates may be responsible for CAR T cell–associated cytopenia. | 115 |
| BMF | Oligoclonal T-cell expansion | CITE-seq, scRNA +TCRαβ-seq | Chromium system, 5′ (10x Genomics) | A patient with BMF after CD19 CAR T-cell therapy for Richter-transformed DLBCL | PBMCs before and after CAR T-cell therapy | Yes | Yes | Oligoclonal T-cell expansion in this patient with BMF after CD19 CAR T-cell therapy. | 116 |
| VEXAS | Inflammasome pathway activation and monocyte dysregulation in VEXAS syndrome | scRNA-seq | Chromium system, 3′ (10x Genomics) | PBMCs | Two patients with VEXAS syndrome, 2 patients with VEXAS syndrome–like disease (severe autoinflammatory disease without UBA1 mutations), 2 patients with MDS, and 2 healthy controls | Yes | N/A | scRNA-seq of PBMCs with dysregulated proinflammatory and cell death signatures in monocytes. | 117 |
| VEXAS | Inflammation and UBA1 mutations in early hematopoiesis in VEXAS. | scRNA + TCR/BCRαβ-seq | Chromium system, 3′ and 5' (10x Genomics) | BMMNCs and Lin−CD34+ HSPCs | Nine patients with VEXAS syndrome and 4 healthy controls | Yes | N/A | Myeloid lineage bias and inflammatory pathway activation occured early in hematopoietic stem cells in VEXAS, and appeared intrinsic to UBA1 mutant cells. | 118 |
| PNH | Hematopoietic cell phenotypes | scRNA-seq | Chromium system, 3′ (10x Genomics) | FAC-sorted CD59+ and CD59− BMMNCs | Three patients and 4 healthy donors | Yes | N/A | Different proportion of hematopoietic cells in PNH BM. | 119 |
| Disease . | Content . | Method . | Platform . | Sample . | Patient cohort . | Disease pathogenesis . | Treatment . | Key finding . | Reference . |
|---|---|---|---|---|---|---|---|---|---|
| AA | T-cell landscape of immune AA | TCRβ-seq and scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | T cells from BM and PB | 153 patients with AA (samples at diagnosis, during remission, and at relapse) | Yes | Yes | Private clonotypes in patients with immune AA may recognize a common antigen; AA signature clonotypes were of effector phenotypes and fluctuate after IST. | 64 |
| AA | Somatic mutations in lymphocytes in immune AA, and phenotypes of STAT3-mutated clones | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Purified T-cell clones | Serial samples from 2 index patients with SAA | Yes | Yes | Somatic mutations were common in patients with AA, enriched in CD8+ T cells, and accumulated most on the JAK-STAT and MAPK pathways; a STAT3-mutated clone was cytotoxic and attenuated by successful IST. | 65 |
| AA | Immune cell phenotypes in pediatric SAA | Single-cell mass cytometry and scRNA-seq | CyTOF and chromium system, 5′ (10x Genomics) | BMMNCs | Nine at diagnosis, 3 after IST, and 4 healthy donors | Yes | Yes | Th17-polarized CD4+ naive T cells with the JAK3/STAT3 pathway activation in pediatric SAA. | 66 |
| AA | Multiomics analysis of AA and a murine model | Publicly available scRNA-seq data (GSE145669) from references, microarray data (GSE3807), and liquid chromatography/mass spectrometry | N/A | Plasma for proteomics; BM-derived HSPCs, CD4+ and CD8+ T cells from the BM and PB (scRNA-seq data from reference 28); and sorted CD3+ T cells (microarray data from GSE3807) | Plasma from 14 patients with SAA and 15 healthy donors | Yes | N/A | Differential proteomics and metabolomics in AA, a population of activated CD8+CD38+ T cells involved in AA. | 67 |
| AA | Single-cell transcriptome of hematopoietic cells and T cells | Full-length scRNA-seq | STRT-seq and full-length Smart-seq2 | BM-derived HSPCs and CD4+ and CD8+ T cells from the BM and PB | Fifteen patients with treatment-naïve AA, including 12 with non-SAA, 3 with SAA, and 4 healthy donors; 5 patients with non-SAA responsive to cyclosporine A plus androgens treatment | Yes | Yes | Selective lineage disruption, alternative splicing, and polyadenylation in AA; cell type–specific ligand–receptor interactions. | 68 |
| AA | NK cell phenotypes in SAA | scRNA-seq | Chromium system, 3′ (10x Genomics) | Sorted NK cells from the BM and PB | Three patients with treatment-naive SAA | Yes | N/A | NK cell subsets altered in SAA. | 70 |
| AA | Single-cell transcriptome of BM cells | scRNA-seq | Chromium system, 3′ (10x Genomics) | BMMNCs and enriched CD34+ cells | Two patients with SAA and 2 healthy donors | Yes | N/A | Dysregulated gene expression of hematopoietic cells, and altered BCR usage and interactions with other cell types. | 77 |
| MDS and CH | Impact of splicing aberrations in human hematopoiesis | Single-cell multiomics: surface protein, gene expression, and RNA splicing | GoT-Splice | CD34+ cells | Six patients with MDS and 2 with CH | Yes | N/A | SF3B1 mutations altered 3' splicing site usage and lineage output in MDS and CH. | 85 |
| MDS | Hematopoietic differentiation and monosomy 7 cells in MDS | scRNA-seq | C1 Fluidigm | Lin−CD34+CD38+ and Lin−CD34+CD38− cells | Five patients with MDS (3 evolved from AA) and 4 healthy donors | Yes | Yes | Distinct differentiation patterns of patients with MDS, and differential gene programs in monosomy 7 cells compared with diploid cells. | 93 |
| MDS | lncRNA landscape in human HSPCs | scRNA-seq | C1 Fluidigm | Lin−CD34+CD38+ and Lin−CD34+CD38− cells | Five patients with MDS (3 evolved from AA) and 4 healthy donors | Yes | Yes | lncRNAs in HSPCs were stage- and cell-type specific, and closely correlated with protein-coding genes in the regulation of hematopoiesis and cell fate decisions; there was differential lncRNA expression in MDS and aneuploid cells. | 94 |
| MDS | HSPCs | scRNA-seq | Chromium system, 3′ (10x Genomics) | Lin− cells from the BM | Five patients with MDS, 2 with secondary AML, and 17 healthy donors (from GSE120221) | Yes | N/A | Abnormal proliferation, RNA metabolism, and ribosome biogenesis in MDS stem cells. | 80 |
| MDS | Stem cell architecture and association with disease progression and response to therapy in MDS | scRNA-seq | Chromium system, 3′ (10x Genomics) | Lin−CD34+ HSPCs | One patient with MDS with a GMP pattern and 1 patient with MDS with a CMP pattern | Yes | Yes | scRNA-seq to validate the distinct differentiation pattern in patients with MDS, and this stem cell architecture was associated with disease progression and response to therapy. | 81 |
| MDS | Frequency and basis for coexistence of splicing factor mutations | scDNA-seq | Mission Bio | BMMNCs | Eleven patients with myeloid neoplasm and double splicing factor mutations | Yes | N/A | Escape from epistasis of RNA splicing factor mutations occured with specific mutation alleles and preservation of 1 wild-type allele. | 86 |
| MDS | Somatic mutations and copy number variations during disease progression and treatment resistance | scDNA-seq | Tapestri Single-cell DNA AML Panel Kit | BM samples | Serial samples of 2 patients with MDS treated with HMA | Yes | Yes | Disease progression and resistance to HMA was accompanied by changes in clone heterogeneity of pathogenic mutations and acquisition of copy number variations. | 87 |
| T-LGLL | T-cell clonotypes and phenotypes in T-LGLL | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Enriched CD45+ cells from PBMCs | Nine patients with T-LGLL and 6 healthy controls | Yes | N/A | T-LGLL clonotypes were more cytotoxic and exhausted than healthy reactive clonotypes; nonleukemic T cell repertoire was also more mature, cytotoxic, and clonally restricted than in other cancers and autoimmune disorders; and leukemic T-LGLL clonotypes shared TCR similarities with their nonleukemic repertoires. | 96 |
| T-LGLL | T-cell clonotypes and phenotypes in T-LGLL and with treatment | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | Enriched CD3+ T cells from PBMCs | Thirteen patients with T-LGLL (12 had paired samples before and 3 or 6 mo after alemtuzumab treatment) and 6 healthy controls | Yes | Yes | There was a lack of common clonotypes of TCR usage in T-LGLL; dysregulated cell survival programs featured with downregulation of apoptosis genes were prominent in T-LGLL cells; apoptosis genes were upregulated after alemtuzumab treatment, more in responders than in nonresponders; and TCR diversity was further skewed after treatment. | 97 |
| CH | Impact of DNMT3A and TET2 mutations on hematopoietic differentiation | Multiomic single-cell analysis: index sorting, scRNA-seq, and genotyping | Target-seq+ | BM samples | Nine CH samples with predicted loss-of-function mutations | Yes | N/A | DNMT3A-mutant and TET2-mutant clones expand in a different manner; and there was a non–cell autonomous impact on WT HSCs in CH. | 98 |
| CH | DNMT3A R882 mutations on hematopoiesis | Multiomic single-cell analysis: capturing genotype, transcriptomes, and methylomes | GoT | CD34+ HSPCs | Three patients with multiple myeloma and DNMT3A R882 mutations | Yes | N/A | DNMT3A R882 mutations perturbed early progenitor states through selective hypomethylation. | 99 |
| CH | Pathogenesis of CH | Simultaneous detection of gene mutations and expression on single cells | Fluidigm C1-HT system | BM-derived HSPCs | Sixteen patients with CH and 16 healthy controls | Yes | N/A | There were non–cell-autonomous phenotypes or an altered BM environment that favored the positive selection of CH− clones. | 100 |
| BMF | Cellular and molecular features associated with CAR T-associated prolonged cytopenia | scRNA + TCRαβ-seq | Chromium system, 5′ (10x Genomics) | BM samples | Sixteen patients with DLBCL who had prolonged cytopenia after treatment with axi-cel | Yes | Yes | Clonally expanded IFN-γ–expressing cytotoxic T cells and an enrichment of IFN signaling within the HSCs of BM aspirates may be responsible for CAR T cell–associated cytopenia. | 115 |
| BMF | Oligoclonal T-cell expansion | CITE-seq, scRNA +TCRαβ-seq | Chromium system, 5′ (10x Genomics) | A patient with BMF after CD19 CAR T-cell therapy for Richter-transformed DLBCL | PBMCs before and after CAR T-cell therapy | Yes | Yes | Oligoclonal T-cell expansion in this patient with BMF after CD19 CAR T-cell therapy. | 116 |
| VEXAS | Inflammasome pathway activation and monocyte dysregulation in VEXAS syndrome | scRNA-seq | Chromium system, 3′ (10x Genomics) | PBMCs | Two patients with VEXAS syndrome, 2 patients with VEXAS syndrome–like disease (severe autoinflammatory disease without UBA1 mutations), 2 patients with MDS, and 2 healthy controls | Yes | N/A | scRNA-seq of PBMCs with dysregulated proinflammatory and cell death signatures in monocytes. | 117 |
| VEXAS | Inflammation and UBA1 mutations in early hematopoiesis in VEXAS. | scRNA + TCR/BCRαβ-seq | Chromium system, 3′ and 5' (10x Genomics) | BMMNCs and Lin−CD34+ HSPCs | Nine patients with VEXAS syndrome and 4 healthy controls | Yes | N/A | Myeloid lineage bias and inflammatory pathway activation occured early in hematopoietic stem cells in VEXAS, and appeared intrinsic to UBA1 mutant cells. | 118 |
| PNH | Hematopoietic cell phenotypes | scRNA-seq | Chromium system, 3′ (10x Genomics) | FAC-sorted CD59+ and CD59− BMMNCs | Three patients and 4 healthy donors | Yes | N/A | Different proportion of hematopoietic cells in PNH BM. | 119 |
AA, aplastic anemia; axi-cel, axicabtagene ciloleucel; BCR, B-cell receptor; CITE-seq, cellular indexing of transcriptomes and epitopes by sequencing; CMP, common myeloid progenitor; CyTOF, cytometry by time of flight; DLBCL, diffuse large B-cell lymphoma; FAC, fluorescence-activated cell; GMP, granulocytic-monocytic progenitor; HMA, hypomethylating agents; IST, immunosuppressive therapy; lncRNA, long noncoding RNA; Lin−, lineage negative; PBMCs, PB mononuclear cells; PNH, paroxysmal nocturnal hemoglobinuria; SAA, severe aplastic anemia; STRT-seq, single-cell tagged reverse transcription sequencing; T-LGLL, T-cell large granular lymphocyte leukemia; WT, wild type.