DOI: 10.5281/zenodo.14624955
title: A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

description: This repository contains R Seurat objects associated with our study titled "A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma". 

Single cell data contained within this object comes from MMRF Immune Atlas Consortium work.The .rds files contains a Seurat object saved with version 4.3. This can be loaded in R with the readRDS command.Two .RDS files are included in this version of the release.



Discovery object: MMRF_ImmuneAtlas_Full_With_Corrected_Censored_Metadata.rds contains all aliquots belonging to the 'discovery' cohort as used in the initial paper. This represents the dataset used for initial clustering, cell annotation, and analysis.

Discovery + Validation object: COMBINED_VALIDATION_MMRF_ImmuneAtlas_Full_Censored_Metadata.rds contains both aliquots belonging to the initial 'discovery' cohort, and aliquots belonging to the 'validation' cohort. The group each cell is derived from is listed under the 'cohort' variable. Labels related to cell annotation, including doublet status, are derived from a label transfer process as described in the paper. Labels for the original 'discovery' cohort are unchanged. UMAPs have been reconstructed with both the discovery and validation cohorts integrated.


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The discovery object contains two assays:



"RNA" - The raw count matrix

"RNA_Batch_Corrected" - Counts adjusted for the combination of 'Study_Site' and 'Batch'.



Analysis should prefer the original RNA assay, unless using pipelines which does not support adjusting for technical covariates.




Currently, the validation object only includes the uncorrected RNA assay.--

The object contains two umaps in the reduction slot:



umap - will render the UMAP for the full object with all cells.

umap.sub -contains the UMAP embeddings for individual 'compartments', as indicated by 'subcluster_V03072023_compartment'


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Each sample has three different identifiers:



public_id



Indicates a specific patient (n=263).

MMRF_####

This is a standard identifier which is used across all MMRF CoMMpass datasets

public_ids can map to multiple d_visit_specimen_ids and aliquot_ids

As of now, all public_ids have a single sample collected at Baseline. 



This can be accessed by filtering for 'collection_event' %in% c("Baseline", "Screening") or VJ_INTERVAL == 'Baseline'





d_visit_specimen_id



Indicates a specific visit by a patient (n=358)

MMRF_####_Y



Y is a number indicate that this is the 'Y' sample obtained from said patient. This does not correspond to a specific timepoint.



This is a standard identifier, which is used across all MMRF CoMMpass datasets

The purpose of the visit is indicated in 'collection_event' (Baseline, Relapse, Remmission, etc.). The approximate interval the visit corresponds to is in "VJ_INTERVAL"

d_visit_specimen_id uniquely maps to one public_id

d_visit_specimen_id can map to multiple aliquot_ids



aliquot_id



Refers to the specific bone marrow aliquot sample processed (n=361)

MMRFA-######

This is a unique identifier for each processed scRNA-seq sample. 

As of now, this uniquely maps to a combination of d_visit_specimen_id, Study_Site, and Batch

As of now, is an identifier specific to the MMRF ImmuneAtlas




Each cell has the following annotation information:



subcluster_V03072023



These refer to an individual cluster derived from 'Seurat'.

Format is 'Compartment'.'Compartment-cluster'.'Compartment-subcluster'



'NkT.2.2', indicates this cell is in the 'Natural Killer + T Cell compartment', was originally part of 'Cluster 2', and then was further separated into a refined subcluster 2.2'

If a parent cluster did not need to be further seprated, the 'Compartment-subcluster' part is omitted (e.g., 'NkT.6')



As of now, this uniquely maps to a specific cellID_short annotation.

Clustering was done on a per compartment basis



For most immune cell types, clustering was based on embeddings corrected for 'siteXbatch'. For Plasma, clustering was performed on embeddings corrected on a per-sample basis.



In the combined validation object, DISCOVERY.subcluster_V03072023 will contain values only for the discovery cohort, and have NA values for validation samples.



subcluster_V03072023_compartment



These refer to one of five major compartments as identified roughly on the original UMAP. Clustering was performed on a per-compartment basis following a first pass rough annotation.

The possible compartments are



NkT (T cell + Natural Killer Cells)

Myeloid (Monocytes, Macrophages, Dendritic cells, Neutrophil/Granulocyte populations)

BEry (B Cell, Erythroblasts, bone marrow progenitor populations, pDCs)

Ery (Erythrocyte population)

Plasma (Plasma cell populations)



Each compartment has it's own UMAP generated, which can be accessed in the 'umap.sub' reduction

One cluster was isolated from all other populations, and was not assigned to a compartment. This cluster is labeled as 'Full.23'.

In the combined validation object, DISCOVERY.subcluster_V03072023_compartment will contain values only for the discovery cohort, and have NA values for validation samples.



cellID_short



This is the individual annotation for each cluster.

Please see the 'Cell Population Annotation Dictionary' for further details.

If different seurat clusters were assigned similar annotations, the celltype annotation will be appended with a distinct cluster gene, or with '_b', '_c'



lineage_group



This is an annotation driven grouping of clusters into major immune populations, as shown in Figure 2.

This includes "CD8", "CD4", "M" (Myeloid), "B" (B cell), "E" (Erythroid), "P" (Plasma), "Other" (HSC, Fibro, pDC_a), "LQ" (Doublet)



isDoublet



This is a binary 'True' or 'False' derived from manual review of clusters following doublet analysis, as described in the paper.

True indicates the cluster was determined to be a doublet population.

This is derived from 'doublet_pred', in which 'dblet_cluster' and 'poss_dblet_cluster' were flagged as doublet populations for subsequent analysis.

In the validation object, the doublet status of new samples were inferred by if label transfer from the discovery cohort mapped the cell from the new sample as one of the previously identified doublet populations. The raw doublet scores from doublet finder, pegasus, or scrublet, are not included in this release.




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Each sample has the following information indicating shipment batches, for batch correction



Study_Site



The center which processed a specific aliquot_id

EMORY, MSSM, WashU, MAYO



Batch



The shipment batch the sample was associated with

Valued 1 to 3 for EMORY, MSSM, MAYO, and 1 to 4 for WashU



siteXbatch



A combination of the above to variables, to be used for batch correction



(Combined Validation Object only): cohort



Indicates if the sample was involved in the 'discovery' cohort, or 'validation' cohort. Samples in the 'validation' cohort will have labels inferred from label mapping




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Each public_id has limited demographic information based on publicly available information in the MMRF CoMMpass study. 



d_pt_sex



Patient sex (not self-identified). Male or Female



d_pt_race_1



Patient self-identified race



d_pt_ethnicity



Patient self-identified ethnicity



d_dx_amm_age



Patient age at diagnosis. 

Not reported for patients above 90 at diagnosis



d_dx_amm_bmi



Patient BMI at diagnosis



d_pt_height_cm



Patient height at diagnosis, in centimeters.



d_dx_amm_weight_kg



Patient weight at diagnosis, in kilograms




d_specimen_visit_id contains two data points providing limited information about the visit



collection_event



Description of why the sample was collected



e.g., 'Baseline' and 'Screening' indicates the sample was obtained prior to therapy

'Relapse/Progression' indicates the sample was collected due to disease progression based on clinical assessment

'Remission/Response' indicates the sample was collected due to patient entering remission based on clinical assessment

Samples may be collected for reasons independent of the above, such as 'Pre' or 'Post' ASCT, or for other unspecified reasons





VJ_INTERVAL



Indicates the rough interval following start of therapy the sample is assigned to



"Baseline", "Month 3", "Year 2", etc.






All the single-cell raw data, along with outcome and cytogenetic information, is available at MMRF’s VLAB shared resource. Requests to access these data will be reviewed by data access committee at MMRF and any data shared will be released under a data transfer agreement that will protect the identities of patients involved in the study. Other information from the CoMMpass trial can also generally be requested through the MMRF's Researcher's Gateway: https://research.themmrf.org/