Cited by 55Multiple Myeloma Research and TreatmentsChronic Lymphocytic Leukemia ResearchLymphoma Diagnosis and Treatment

Single cell clonotypic and transcriptional evolution of multiple myeloma precursor disease

Open access
Dang, Minghao, Han, Guangchun, Lee, Hans C., Patel, Krina K., Becnel, Melody R., Wang, Ruiping, Thomas, Sheeba K., Hao, Dapeng +22 more·2023·Cancer Cell

Abstract

Multiple myeloma remains an incurable disease, and the cellular and molecular evolution from precursor conditions, including monoclonal gammopathy of undetermined significance and smoldering multiple myeloma, is incompletely understood. Here, we combine single-cell RNA and B cell receptor sequencing from fifty-two patients with myeloma precursors in comparison with myeloma and normal donors. Our comprehensive analysis reveals early genomic drivers of malignant transformation, distinct transcriptional features, and divergent clonal expansion in hyperdiploid versus non-hyperdiploid samples. Additionally, we observe intra-patient heterogeneity with potential therapeutic implications and identify distinct patterns of evolution from myeloma precursor disease to myeloma. We also demonstrate distinctive characteristics of the microenvironment associated with specific genomic changes in myeloma cells. These findings add to our knowledge about myeloma precursor disease progression, providing valuable insights into patient risk stratification, biomarker discovery, and possible clinical applications.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.ccell.2023.05.007

Cites

5 of 5 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Several patterns of immune dysregulation have been reported in MGUS and SMM using single cell RNA sequencing.

    “Several patterns of dysregulation have been reported using single cell RNA sequencing.82,83,91-93”

    From Evolution of Multiple Myeloma from a Genomic Perspective (2026) · cites this paper as [82]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 48

  1. Alexanian, R., Delasalle, K., Wang, M., Thomas, S., and Weber, D. (2012). Curability of multiple myeloma. Bone Marrow Res. 2012, 916479. https:// doi.org/10.1155/2012/916479. · DOI
  2. Barlogie, B., Mitchell, A., van Rhee, F., Epstein, J., Morgan, G.J., and Crowley, J. (2014). Curing myeloma at last: defining criteria and providing the evidence. Blood 124, 3043-3051. https://doi.org/10.1182/blood- 2014-07-552059. · DOI
  3. Rajkumar, S.V., Dimopoulos, M.A., Palumbo, A., Blade, J., Merlini, G., Mateos, M.V., Kumar, S., Hillengass, J., Kastritis, E., Richardson, P., et al. (2014). International Myeloma Working Group updated criteria for the diagnosis of multiple myeloma. Lancet Oncol. 15, e538-e548. https://doi.org/10.1016/S1470-2045(14)70442-5. · DOI · Paper page
  4. Kunacheewa, C., and Manasanch, E.E. (2020). High-risk smoldering myeloma versus early detection of multiple myeloma: current models, goals of therapy, and clinical implications. Best Pract. Res. Clin. Haematol. 33, 101152. https://doi.org/10.1016/j.beha.2020.101152. · DOI
  5. Dhodapkar, M.V., Sexton, R., Waheed, S., Usmani, S., Papanikolaou, X., Nair, B., Petty, N., Shaughnessy, J.D., Jr., Hoering, A., Crowley, J., et al. (2014). Clinical, genomic, and imaging predictors of myeloma progression from asymptomatic monoclonal gammopathies (SWOG S0120). Blood 123, 78-85. https://doi.org/10.1182/blood-2013-07-515239. · DOI · Paper page
  6. Pawlyn, C., and Morgan, G.J. (2017). Evolutionary biology of high-risk mul- tiple myeloma. Nat. Rev. Cancer 17, 543-556. https://doi.org/10.1038/ nrc.2017.63. · DOI
  7. Morgan, G.J., Walker, B.A., and Davies, F.E. (2012). The genetic architec- ture of multiple myeloma. Nat. Rev. Cancer 12, 335-348. https://doi.org/ 10.1038/nrc3257. · DOI · Paper page
  8. Manier, S., Salem, K.Z., Park, J., Landau, D.A., Getz, G., and Ghobrial, I.M. (2017). Genomic complexity of multiple myeloma and its clinical implica- tions. Nat. Rev. Clin. Oncol. 14, 100-113. https://doi.org/10.1038/nrcli- nonc.2016.122. · DOI
  9. Garcı ´a-Ortiz, A., Rodrı ´guez-Garcı ´a, Y., Encinas, J., Maroto-Martı ´n, E., Castellano, E., Teixido ´, J., and Martı ´nez-Lo ´pez, J. (2021). The role of tumor microenvironment in multiple myeloma development and progression. Cancers 13, 217. https://doi.org/10.3390/cancers13020217. · DOI · Paper page
  10. Isola, I., Braso ´-Maristany, F., Moreno, D.F., Mena, M.P., Oliver-Calders, A., Pare ´, L., Rodrı ´guez-Lobato, L.G., Martin-Antonio, B., Cibeira, M.T., Blade ´, J., et al. (2021). Gene expression analysis of the bone marrow microenvironment reveals distinct immunotypes in smoldering multiple myeloma associated to progression to symptomatic disease. Front. Immunol. 12, 792609. https://doi.org/10.3389/fimmu.2021.792609. · DOI
  11. Geng, S., Wang, J., Zhang, X., Zhang, J.J., Wu, F., Pang, Y., Zhong, Y., Wang, J., Wang, W., Lyu, X., et al. (2020). Single-cell RNA sequencing re- veals chemokine self-feeding of myeloma cells promotes extramedullary metastasis. FEBS Lett. 594, 452-465. https://doi.org/10.1002/1873- 3468.13623. · DOI
  12. Zavidij, O., Haradhvala, N.J., Mouhieddine, T.H., Sklavenitis-Pistofidis, R., Cai, S., Reidy, M., Rahmat, M., Flaifel, A., Ferland, B., Su, N.K., et al. (2020). Single-cell RNA sequencing reveals compromised immune micro- environment in precursor stages of multiple myeloma. Nat. Cancer 1, 493-506. https://doi.org/10.1038/s43018-020-0053-3. · DOI · Paper page
  13. Ryu, D., Kim, S.J., Hong, Y., Jo, A., Kim, N., Kim, H.J., Lee, H.O., Kim, K., and Park, W.Y. (2020). Alterations in the transcriptional programs of myeloma cells and the microenvironment during extramedullary progres- sion affect proliferation and immune evasion. Clin. Cancer Res. 26, 935-944. https://doi.org/10.1158/1078-0432.CCR-19-0694. · DOI
  14. Jang, J.S., Li, Y., Mitra, A.K., Bi, L., Abyzov, A., van Wijnen, A.J., Baughn, L.B., Van Ness, B., Rajkumar, V., Kumar, S., and Jen, J. (2019). Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood Cancer J. 9, 2. https://doi.org/10.1038/s41408-018-0160-x. · DOI
  15. Ledergor, G., Weiner, A., Zada, M., Wang, S.Y., Cohen, Y.C., Gatt, M.E., Snir, N., Magen, H., Koren-Michowitz, M., Herzog-Tzarfati, K., et al. (2018). Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat. Med. 24, 1867-1876. https://doi.org/ 10.1038/s41591-018-0269-2. · DOI · Paper page
  16. Liu, R., Gao, Q., Foltz, S.M., Fowles, J.S., Yao, L., Wang, J.T., Cao, S., Sun, H., Wendl, M.C., Sethuraman, S., et al. (2021). Co-evolution of tumor and immune cells during progression of multiple myeloma. Nat. Commun. 12, 2559. https://doi.org/10.1038/s41467-021-22804-x. · DOI
  17. Merz, M., Merz, A.M.A., Wang, J., Wei, L., Hu, Q., Hutson, N., Rondeau, C., Celotto, K., Belal, A., Alberico, R., et al. (2022). Deciphering spatial genomic heterogeneity at a single cell resolution in multiple myeloma. Nat. Commun. 13, 807. https://doi.org/10.1038/s41467-022-28266-z. · DOI
  18. Tirier, S.M., Mallm, J.P., Steiger, S., Poos, A.M., Awwad, M.H.S., Giesen, N., Casiraghi, N., Susak, H., Bauer, K., Baumann, A., et al. (2021). Subclone-specific microenvironmental impact and drug response in re- fractory multiple myeloma revealed by single-cell transcriptomics. Nat. Commun. 12, 6960. https://doi.org/10.1038/s41467-021-26951-z. · DOI
  19. Abbas, H.A., Hao, D., Tomczak, K., Barrodia, P., Im, J.S., Reville, P.K., Alaniz, Z., Wang, W., Wang, R., Wang, F., et al. (2021). Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy. Nat. Commun. 12, 6071. https://doi.org/10. 1038/s41467-021-26282-z. · DOI
  20. Sinjab, A., Han, G., Treekitkarnmongkol, W., Hara, K., Brennan, P.M., Dang, M., Hao, D., Wang, R., Dai, E., Dejima, H., et al. (2021). Resolving the spatial and cellular architecture of lung adenocarcinoma by multire- gion single-cell sequencing. Cancer Discov. 11, 2506-2523. https://doi. org/10.1158/2159-8290.CD-20-1285. · DOI
  21. Wang, R., Dang, M., Harada, K., Han, G., Wang, F., Pool Pizzi, M., Zhao, M., Tatlonghari, G., Zhang, S., Hao, D., et al. (2021). Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Nat. Med. 27, 141-151. https://doi.org/10.1038/ s41591-020-1125-8. · DOI
  22. Zhang, S., Jiang, V.C., Han, G., Hao, D., Lian, J., Liu, Y., Zhang, R., McIntosh, J., Wang, R., Dang, M., et al. (2021). Longitudinal single-cell profiling reveals molecular heterogeneity and tumor-immune evolution in refractory mantle cell lymphoma. Nat. Commun. 12, 2877. https://doi. org/10.1038/s41467-021-22872-z. · DOI
  23. Miller, C., Yesil, J., Derome, M., Donnelly, A., Marrian, J., McBride, K., CoMMpass Network, M., Auclair, D., and Keats, J.J. (2016). A comparison of clinical FISH and sequencing based FISH estimates in multiple myeloma: an Mmrf commpass analysis. Blood 128, 374. https://doi.org/ 10.1182/blood.V128.22.374.374. · DOI
  24. Van Wier, S., Braggio, E., Baker, A., Ahmann, G., Levy, J., Carpten, J.D., and Fonseca, R. (2013). Hypodiploid multiple myeloma is characterized by more aggressive molecular markers than non-hyperdiploid multiple myeloma. Haematologica 98, 1586-1592. https://doi.org/10.3324/hae- matol.2012.081083. · DOI
  25. Chng, W.J., Kumar, S., Vanwier, S., Ahmann, G., Price-Troska, T., Henderson, K., Chung, T.H., Kim, S., Mulligan, G., Bryant, B., et al. (2007). Molecular dissection of hyperdiploid multiple myeloma by gene expression profiling. Cancer Res. 67, 2982-2989. https://doi.org/10. 1158/0008-5472.CAN-06-4046. · DOI
  26. Sanchez, E., Li, M., Kitto, A., Li, J., Wang, C.S., Kirk, D.T., Yellin, O., Nichols, C.M., Dreyer, M.P., Ahles, C.P., et al. (2012). Serum B-cell matu- ration antigen is elevated in multiple myeloma and correlates with disease status and survival. Br. J. Haematol. 158, 727-738. https://doi.org/10. 1111/j.1365-2141.2012.09241.x. · DOI
  27. Elkins, K., Zheng, B., Go, M., Slaga, D., Du, C., Scales, S.J., Yu, S.F., McBride, J., de Tute, R., Rawstron, A., et al. (2012). FcRL5 as a target of antibody-drug conjugates for the treatment of multiple myeloma. Mol. Cancer Ther. 11, 2222-2232. https://doi.org/10.1158/1535-7163.Mct- 12-0087. · DOI
  28. Neri, P., Ren, L., Azab, A.K., Brentnall, M., Gratton, K., Klimowicz, A.C., Lin, C., Duggan, P., Tassone, P., Mansoor, A., et al. (2011). Integrin beta7-mediated regulation of multiple myeloma cell adhesion, migration, and invasion. Blood 117, 6202-6213. https://doi.org/10.1182/blood- 2010-06-292243. · DOI
  29. Robbiani, D.F., Colon, K., Ely, S., Ely, S., Chesi, M., and Bergsagel, P.L. (2007). Osteopontin dysregulation and lytic bone lesions in multiple myeloma. Hematol. Oncol. 25, 16-20. https://doi.org/10.1002/hon.803. · DOI
  30. De Vos, J., Couderc, G., Tarte, K., Jourdan, M., Requirand, G., Delteil, M.C., Rossi, J.F., Mechti, N., and Klein, B. (2001). Identifying intercellular signaling genes expressed in malignant plasma cells by using comple- mentary DNA arrays. Blood 98, 771-780. https://doi.org/10.1182/blood. V98.3.771. · DOI
  31. Bret, C., Hose, D., Reme, T., Sprynski, A.C., Mahtouk, K., Schved, J.F., Quittet, P., Rossi, J.F., Goldschmidt, H., and Klein, B. (2009). Expression of genes encoding for proteins involved in heparan sulphate and chon- droitin sulphate chain synthesis and modification in normal and malignant plasma cells. Br. J. Haematol. 145, 350-368. https://doi.org/10.1111/j. 1365-2141.2009.07633.x. · DOI
  32. Ohguchi, H., Hideshima, T., Bhasin, M.K., Gorgun, G.T., Santo, L., Cea, M., Samur, M.K., Mimura, N., Suzuki, R., Tai, Y.T., et al. (2016). The KDM3A-KLF2-IRF4 axis maintains myeloma cell survival. Nat. Commun. 7, 10258. https://doi.org/10.1038/ncomms10258. · DOI
  33. Rojas, E.A., Corchete, L.A., Mateos, M.V., Garcı ´a-Sanz, R., Misiewicz- Krzeminska, I., and Gutie ´rrez, N.C. (2019). Transcriptome analysis reveals significant differences between primary plasma cell leukemia and multiple myeloma even when sharing a similar genetic background. Blood Cancer J. 9, 90. https://doi.org/10.1038/s41408-019-0253-1. · DOI
  34. Rendtlew Danielsen, J.M., Knudsen, L.M., Dahl, I.M., Lodahl, M., and Rasmussen, T. (2007). Dysregulation of CD47 and the ligands thrombo- spondin 1 and 2 in multiple myeloma. Br. J. Haematol. 138, 756-760. https://doi.org/10.1111/j.1365-2141.2007.06729.x. · DOI
  35. Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N.J., Livak, K.J., Mikkelsen, T.S., and Rinn, J.L. (2014). The dy- namics and regulators of cell fate decisions are revealed by pseudotem- poral ordering of single cells. Nat. Biotechnol. 32, 381-386. https://doi. org/10.1038/nbt.2859. · DOI · Paper page
  36. Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H.A., and Trapnell, C. (2017). Reversed graph embedding resolves complex single-cell trajec- tories. Nat. Methods 14, 979-982. https://doi.org/10.1038/nmeth.4402. · DOI · Paper page
  37. Qiu, X., Hill, A., Packer, J., Lin, D., Ma, Y.A., and Trapnell, C. (2017). Single- cell mRNA quantification and differential analysis with Census. Nat. Methods 14, 309-315. https://doi.org/10.1038/Nmeth.4150. · DOI
  38. Lakshman, A., Rajkumar, S.V., Buadi, F.K., Binder, M., Gertz, M.A., Lacy, M.Q., Dispenzieri, A., Dingli, D., Fonder, A.L., Hayman, S.R., et al. (2018). Risk stratification of smoldering multiple myeloma incorporating revised IMWG diagnostic criteria. Blood Cancer J. 8, 59. https://doi.org/10. 1038/s41408-018-0077-4. · DOI
  39. Efremova, M., Vento-Tormo, M., Teichmann, S.A., and Vento-Tormo, R. (2020). CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat. Protoc. 15, 1484-1506. https://doi.org/10.1038/s41596-020-0292-x. · DOI · Paper page
  40. Melchor, L., Brioli, A., Wardell, C.P., Murison, A., Potter, N.E., Kaiser, M.F., Fryer, R.A., Johnson, D.C., Begum, D.B., Hulkki Wilson, S., et al. (2014). Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma. Leukemia 28, 1705-1715. https://doi.org/10.1038/leu.2014.13. · DOI
  41. Jacobi, B., Stroeher, L., Leuchtner, N., Echchannaoui, H., Desuki, A., Kuerzer, L., Habermeier, A., Antunes, E., Amann, E., Bomalaski, J., et al. (2015). Interfering with arginine metabolism as a new treatment strategy for multiple myeloma. Blood 126, 3005. https://doi.org/10.1182/blood. V126.23.3005.3005. · DOI
  42. Windschmitt, J., Jacobi, B., B€ ulb€ ul, Y., Sester, L., Tappe, J., Hiebel, C., Behl, C., Theobald, M., and Munder, M. (2018). Arginine depletion in com- bination with canavanine supplementation induces massive cell death in myeloma cells by interfering with their protein metabolism and bypassing potential rescue mechanisms. Blood 132, 3205. https://doi.org/10.1182/ blood-2018-99-113396. · DOI
  43. Butler, A., Hoffman, P., Smibert, P., Papalexi, E., and Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411-420. https://doi. org/10.1038/nbt.4096. · DOI · Paper page
  44. Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner, M., Loh, P.R., and Raychaudhuri, S. (2019). Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289-1296. https://doi.org/10.1038/s41592- 019-0619-0. · DOI · Paper page
  45. Becht, E., McInnes, L., Healy, J., Dutertre, C.A., Kwok, I.W.H., Ng, L.G., Ginhoux, F., and Newell, E.W. (2018). Dimensionality reduction for visual- izing single-cell data using UMAP. Nat. Biotechnol. 37, 38-44. https://doi. org/10.1038/nbt.4314. · DOI · Paper page
  46. Azizi, E., Carr, A.J., Plitas, G., Cornish, A.E., Konopacki, C., Prabhakaran, S., Nainys, J., Wu, K., Kiseliovas, V., Setty, M., et al. (2018). Single-cell map of diverse immune phenotypes in the breast tumor microenvironment. Cell 174, 1293-1308.e36. https://doi.org/10.1016/j.cell.2018.05.060. · DOI · Paper page
  47. Cillo, A.R., K€ urten, C.H.L., Tabib, T., Qi, Z., Onkar, S., Wang, T., Liu, A., Duvvuri, U., Kim, S., Soose, R.J., et al. (2020). Immune landscape of viral- and carcinogen-driven head and neck cancer. Immunity 52, 183-199.e9. https://doi.org/10.1016/j.immuni.2019.11.014. · DOI
  48. Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001). Controlling the false discovery rate in behavior genetics research. Behav. Brain Res. 125, 279-284. https://doi.org/10.1016/s0166-4328(01)00297-2. · DOI · Paper page

Cited by

Sorted by citations

Authors
Dang, M., Han, G., Lee, H. C., Patel, K. K., Becnel, M. R., Wang, R., Thomas, S. K., Hao, D., Chu, Y., Weber, D. M., Lin, P., Lutter-Berka, Z., Berrios Nolasco, D. A., Huang, M., Bansal, H., Song, X., Zhang, J., Futreal, A., Moreno Rueda, L. Y., Symer, D. E., Green, M. R., Rojas Hernandez, C. M., Kroll, M., Afshar-Khargan, V., Ndacayisaba, L. J., Kuhn, P., Neelapu, S. S., Orlowski, R. Z., Wang, L., & Manasanch, E. E.
Affiliations
  • The University of Texas MD Anderson Cancer Center (US)
  • University of Southern California (US)
Corresponding author
  • Wang, Linghua
  • Manasanch, Elisabet E.
Venue
Cancer Cell
Publisher
Elsevier BV
Published
2023-06
Volume
41
Issue
6
Pages
1032-1047.e4
ISSN
1535-6108 (ISSN-L)
OpenAlex
W4380321863
Cited by
55
References
5
Citations by year
2026: 19 · 2025: 21 · 2024: 12 · 2023: 3
FWCI
11.36
Type
journal article
Language
en
Open access
Locations
  • Cancer Cell (publishedVersion)
  • SSRN Electronic Journal (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Digital Commons-TMC (Texas Medical Center) (submittedVersion)
Funders
  • Dr. Miriam and Sheldon G. Adelson Medical Research Foundation
  • National Institutes of Health (1S10OD024977-01)
  • University of Texas MD Anderson Cancer Center (P30 CA016672)
  • Leukemia & Lymphoma Society (SCOR-12206-17)
Topics
  • Health Sciences › Medicine › Hematology › Multiple Myeloma Research and Treatments
  • Health Sciences › Medicine › Genetics › Chronic Lymphocytic Leukemia Research
  • Health Sciences › Medicine › Pathology and Forensic Medicine › Lymphoma Diagnosis and Treatment
Keywords
multiple myeloma, monoclonal gammopathy of undetermined significance, smoldering multiple myeloma, clonal evolution, B cell receptor repertoire, hyperdiploidy, malignant transformation, intrapatient heterogeneity, tumor microenvironment, risk stratification, biomarkers
MeSH terms
Smoldering Multiple Myeloma, Aneuploidy, Humans, Multiple Myeloma, Disease Progression, Biomedical Research, Tumor Microenvironment

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review