A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma

This repository contains R Seurat object 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 file contains a Seurat object saved with version 4.3. This can be loaded in R with the readRDS command.The 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.

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'

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.

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'.

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.

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

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/