Table 1. List of single-cell genomics... | American Society of Hematology

Table 1.

List of single-cell genomics papers published since 2016

PMID	Authors	Cell types evaluated with single-cell genomics	Single-cell platforms used	Time point	Tags
36026513¹⁰²	Dhodapkar et al, 2023	BMMC	scRNA, scTCR, scCITE, CyTOF	Before and after anti-BCMA treatment	Microenvironment, MM cells, CART
36702834⁹¹	Pilcher et al, 2023	CD138⁻	scRNA	Diagnosis	Microenvironment, rapid progression
36379208⁹⁰	Sklavenitis-Pistofidis et al, 2022	CD138⁻ BMMC, PB	scRNA, scTCR, CyTOF	Baseline, cycle 9, end of the treatment	Immunotherapy, microenvironment, immune normalization
36396631⁹⁸	Boiarsky et al, 2022	CD138⁺	scRNA	MGUS, SMM, MM, NPC	Transcriptional signature, progression
36252999¹⁰³	Kehl et al, 2022	BMMC, PB	scRNA, scCITE		Microenvironment, IgE, T cells
36163550¹⁰⁴	Gao et al, 2022	CD138⁺	scRNA		CNV
36343306⁶⁶	Lannes et al, 2022	CD138⁺	scDNA	SMM, NDMM	CNV, shallow seq
36131282⁹²	Liang et al, 2022	BMMC	scRNA	NDMM, RRMM	Clonal evolution, microenvironment, CNA
36122410¹⁰⁵	Welters et al, 2022	BM T cells	scRNA, scCITE, scVDJ	NDMM	T cells, clonal expansion
36969740¹⁰⁶	Yao et al, 2022	CD138⁻	scRNA, scCITE, CyTOF	NDMM	Microenvironment, classification by progression time
35977111⁸³	Schinke et al, 2022	CD138⁻	scRNA, scTCR	MGUS, SMM, NDMM	Microenvironment, disease progression
35992084⁶⁹	Masuda et al, 2022	CD138⁺	scRNA	NDMM, RRMM	Drug-response, longitudinal samples
35264575⁷⁰	Kumar et al, 2022	CD138⁺	scRNA	HMCL	Drug resistance
35145077⁶⁵	Merz et al, 2022	CD138⁺ (BM and OL)	scRNA	NDMM, RRMM	Spatial heterogeneity
35646666¹⁰⁷	Kumar et al, 2022	CD138⁺, HMCL	CyTOF	MM	PI, IMID, drug resistance
34518309⁷¹	Waldschmidt et al, 2021	CD138⁺	scRNA	RRMM	BRAF, drug resistance
34845188⁸⁷	Tirier et al, 2021	CD138⁺, CD138⁻	scRNA	RRMM	Drug response, microenvironment
34732728¹⁰⁸	Croucher et al, 2021	BM of mice	scRNA	Early, intermediate, and active MM	Vκ∗MYC mice, CNV
34675390⁶⁷	Frede et al, 2021	CD138⁺, CD45⁺	scRNA, scATAC	RRMM, NPC	Transcriptional reprogramming under treatment, immunotherapeutic vulnerabilities, integrative analysis
34133718⁶⁸	Alameda et al, 2021	PCs from SLO, PB, and BM	scRNA	MGUS, AL, MM	Transcriptional rewiring, AL, PC malignancy comparison
33602683¹⁰⁹	Cho et al, 2021	CD56⁺ NK cells	scRNA	NDMM	Antibody-dependent cellular cytotoxicity, NK cells, daratumumab
34017122⁸⁶	de Jong et al, 2021	Nonhematopoietic microenvironment, CD38⁺ and CD38^– immune microenvironments	scRNA	NDMM, NPC	Stromal cells, microenvironment, iMSC
33963182⁵⁷	Liu et al, 2021	BMMC	scRNA	SMM, NDMM, RRMM	Longitudinal samples, clonal evolution, microenvironment, integrative analysis
33619369⁷²	Cohen et al, 2021	CD138⁺	scRNA	NDMM, RRMM, NPC	Longitudinal samples, therapeutic resistance
33558511⁶⁰	Samur et al, 2021	BMMC	scRNA	RRMM	CART, immunotherapy resistance, longitudinal samples, microenvironment
33619368⁶¹	Da Via et al, 2021	BMMC	scRNA	RRMM	CART, immunotherapy resistance, longitudinal samples
32693406⁵⁹	Goicoechea et al, 2021	8-color EuroFlow NGF antibody panel	scRNA	NDMM	Standard vs high-risk MM, transcriptome
32299093⁶⁴	Maia et al, 2020	CD34⁺ HPCs	Targeted scDNA	NDMM	Myelodysplastic syndrome, SNVs
31595039⁶³	Garcés et al, 2020	8-color EuroFlow NGF antibody panel	scRNA	NDMM	Circulating cells, BM vs PB, transcriptome
33409501⁸¹	Zavidij et al, 2020	CD138⁻, CD45⁺	scRNA	MGUS, SMM, NDMM, NPC	Microenvironment, precursor conditions
31988495¹¹⁰	Teh et al, 2020	CD138⁺, HMCL	CyTOF	Before and after treatment	Resistance, synergistic drug combination
31013254⁸²	Bailur et al, 2019	BMMC, CD138⁻	scRNA, CyTOF	MGUS,NDMM, NPC	T cells, myeloid cells, microenvironment
30607001¹¹¹	Jang et al, 2019	CD138⁺	scRNA	MGUS, SMM, NDMM, RRMM	Disease progression, transcriptomic signatures
31462637¹¹²	Kourelis et al, 2019	BMMC, PB	CyTOF	MM, MGUS, SMM, AL	Microenvironment, immune escape, PB vs BM
30523328⁵⁸	Ledergor et al, 2018	CD138⁺	scRNA	MGUS, SMM, NDMM, AL, NPC	Circulating cells, BM vs PB, heterogeneity, subclones, CNA, BCR
27807282⁶²	Lohr et al, 2016	CD138⁺	scRNA, targeted scDNA	MGUS, NDMM	Circulating cells, BM vs PB, heterogeneity, subclones, CNA, SNV
25711758¹¹³	Hansmann et al, 2015	PB	CyTOF	MM, MGUS, AL	PBMC, immune cells

PMID	Authors	Cell types evaluated with single-cell genomics	Single-cell platforms used	Time point	Tags
36026513¹⁰²	Dhodapkar et al, 2023	BMMC	scRNA, scTCR, scCITE, CyTOF	Before and after anti-BCMA treatment	Microenvironment, MM cells, CART
36702834⁹¹	Pilcher et al, 2023	CD138⁻	scRNA	Diagnosis	Microenvironment, rapid progression
36379208⁹⁰	Sklavenitis-Pistofidis et al, 2022	CD138⁻ BMMC, PB	scRNA, scTCR, CyTOF	Baseline, cycle 9, end of the treatment	Immunotherapy, microenvironment, immune normalization
36396631⁹⁸	Boiarsky et al, 2022	CD138⁺	scRNA	MGUS, SMM, MM, NPC	Transcriptional signature, progression
36252999¹⁰³	Kehl et al, 2022	BMMC, PB	scRNA, scCITE		Microenvironment, IgE, T cells
36163550¹⁰⁴	Gao et al, 2022	CD138⁺	scRNA		CNV
36343306⁶⁶	Lannes et al, 2022	CD138⁺	scDNA	SMM, NDMM	CNV, shallow seq
36131282⁹²	Liang et al, 2022	BMMC	scRNA	NDMM, RRMM	Clonal evolution, microenvironment, CNA
36122410¹⁰⁵	Welters et al, 2022	BM T cells	scRNA, scCITE, scVDJ	NDMM	T cells, clonal expansion
36969740¹⁰⁶	Yao et al, 2022	CD138⁻	scRNA, scCITE, CyTOF	NDMM	Microenvironment, classification by progression time
35977111⁸³	Schinke et al, 2022	CD138⁻	scRNA, scTCR	MGUS, SMM, NDMM	Microenvironment, disease progression
35992084⁶⁹	Masuda et al, 2022	CD138⁺	scRNA	NDMM, RRMM	Drug-response, longitudinal samples
35264575⁷⁰	Kumar et al, 2022	CD138⁺	scRNA	HMCL	Drug resistance
35145077⁶⁵	Merz et al, 2022	CD138⁺ (BM and OL)	scRNA	NDMM, RRMM	Spatial heterogeneity
35646666¹⁰⁷	Kumar et al, 2022	CD138⁺, HMCL	CyTOF	MM	PI, IMID, drug resistance
34518309⁷¹	Waldschmidt et al, 2021	CD138⁺	scRNA	RRMM	BRAF, drug resistance
34845188⁸⁷	Tirier et al, 2021	CD138⁺, CD138⁻	scRNA	RRMM	Drug response, microenvironment
34732728¹⁰⁸	Croucher et al, 2021	BM of mice	scRNA	Early, intermediate, and active MM	Vκ∗MYC mice, CNV
34675390⁶⁷	Frede et al, 2021	CD138⁺, CD45⁺	scRNA, scATAC	RRMM, NPC	Transcriptional reprogramming under treatment, immunotherapeutic vulnerabilities, integrative analysis
34133718⁶⁸	Alameda et al, 2021	PCs from SLO, PB, and BM	scRNA	MGUS, AL, MM	Transcriptional rewiring, AL, PC malignancy comparison
33602683¹⁰⁹	Cho et al, 2021	CD56⁺ NK cells	scRNA	NDMM	Antibody-dependent cellular cytotoxicity, NK cells, daratumumab
34017122⁸⁶	de Jong et al, 2021	Nonhematopoietic microenvironment, CD38⁺ and CD38^– immune microenvironments	scRNA	NDMM, NPC	Stromal cells, microenvironment, iMSC
33963182⁵⁷	Liu et al, 2021	BMMC	scRNA	SMM, NDMM, RRMM	Longitudinal samples, clonal evolution, microenvironment, integrative analysis
33619369⁷²	Cohen et al, 2021	CD138⁺	scRNA	NDMM, RRMM, NPC	Longitudinal samples, therapeutic resistance
33558511⁶⁰	Samur et al, 2021	BMMC	scRNA	RRMM	CART, immunotherapy resistance, longitudinal samples, microenvironment
33619368⁶¹	Da Via et al, 2021	BMMC	scRNA	RRMM	CART, immunotherapy resistance, longitudinal samples
32693406⁵⁹	Goicoechea et al, 2021	8-color EuroFlow NGF antibody panel	scRNA	NDMM	Standard vs high-risk MM, transcriptome
32299093⁶⁴	Maia et al, 2020	CD34⁺ HPCs	Targeted scDNA	NDMM	Myelodysplastic syndrome, SNVs
31595039⁶³	Garcés et al, 2020	8-color EuroFlow NGF antibody panel	scRNA	NDMM	Circulating cells, BM vs PB, transcriptome
33409501⁸¹	Zavidij et al, 2020	CD138⁻, CD45⁺	scRNA	MGUS, SMM, NDMM, NPC	Microenvironment, precursor conditions
31988495¹¹⁰	Teh et al, 2020	CD138⁺, HMCL	CyTOF	Before and after treatment	Resistance, synergistic drug combination
31013254⁸²	Bailur et al, 2019	BMMC, CD138⁻	scRNA, CyTOF	MGUS,NDMM, NPC	T cells, myeloid cells, microenvironment
30607001¹¹¹	Jang et al, 2019	CD138⁺	scRNA	MGUS, SMM, NDMM, RRMM	Disease progression, transcriptomic signatures
31462637¹¹²	Kourelis et al, 2019	BMMC, PB	CyTOF	MM, MGUS, SMM, AL	Microenvironment, immune escape, PB vs BM
30523328⁵⁸	Ledergor et al, 2018	CD138⁺	scRNA	MGUS, SMM, NDMM, AL, NPC	Circulating cells, BM vs PB, heterogeneity, subclones, CNA, BCR
27807282⁶²	Lohr et al, 2016	CD138⁺	scRNA, targeted scDNA	MGUS, NDMM	Circulating cells, BM vs PB, heterogeneity, subclones, CNA, SNV
25711758¹¹³	Hansmann et al, 2015	PB	CyTOF	MM, MGUS, AL	PBMC, immune cells

Papers are ordered chronologically, and cell types analyzed with single-cell platforms are listed. Tags are globally categorizing the papers based on the research question addressed.

BMMC, bone marrow mononuclear cells; CART, chimeric antigen receptor T-cell therapy; CNV, copy number variant; HMCL, human myeloma cell lines; IgE, immunoglobulin E; IMID, immunomodulatory derivatives; iMSC, inflammatory mesenchymal stromal cells; NDMM, newly-diagnosed MM; NGF, next-generation flow; NPC, normal plasma cell; OL, osteolytic lesion; PMID, PubMed identification number; SLO, secondary lymphoid organ.

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