Single-cell map of diverse immune phenotypes in the acute myeloid leukemia microenvironment

Abstract Background Knowledge of immune cell phenotypes, function, and developmental trajectory in acute myeloid leukemia (AML) microenvironment is essential for understanding mechanisms of evading immune surveillance and immunotherapy response of targeting special microenvironment components. Methods Using a single-cell RNA sequencing (scRNA-seq) dataset, we analyzed the immune cell phenotypes, function, and developmental trajectory of bone marrow (BM) samples from 16 AML patients and 4 healthy donors, but not AML blasts. Results We observed a significant difference between normal and AML BM immune cells. Here, we defined the diversity of dendritic cells (DC) and macrophages in different AML patients. We also identified several unique immune cell types including T helper cell 17 (TH17)-like intermediate population, cytotoxic CD4+ T subset, T cell: erythrocyte complexes, activated regulatory T cells (Treg), and CD8+ memory-like subset. Emerging AML cells remodels the BM immune microenvironment powerfully, leads to immunosuppression by accumulating exhausted/dysfunctional immune effectors, expending immune-activated types, and promoting the formation of suppressive subsets. Conclusion Our results provide a comprehensive AML BM immune cell census, which can help to select pinpoint targeted drug and predict efficacy of immunotherapy.

Download Full-text

Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

Nature Communications ◽

10.1038/s41467-021-26282-z ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hussein A. Abbas ◽

Dapeng Hao ◽

Katarzyna Tomczak ◽

Praveen Barrodia ◽

Jin Seon Im ◽

...

Keyword(s):

Bone Marrow ◽

Acute Myeloid Leukemia ◽

T Cell ◽

Single Cell ◽

T Cell Receptor ◽

Myeloid Leukemia ◽

Cell Receptor ◽

T Cell Phenotypes ◽

Cell Phenotypes ◽

Acute Myeloid

AbstractIn contrast to the curative effect of allogenic stem cell transplantation in acute myeloid leukemia via T cell activity, only modest responses are achieved with checkpoint-blockade therapy, which might be explained by T cell phenotypes and T cell receptor (TCR) repertoires. Here, we show by paired single-cell RNA analysis and TCR repertoire profiling of bone marrow cells in relapsed/refractory acute myeloid leukemia patients pre/post azacytidine+nivolumab treatment that the disease-related T cell subsets are highly heterogeneous, and their abundance changes following PD-1 blockade-based treatment. TCR repertoires expand and primarily emerge from CD8+ cells in patients responding to treatment or having a stable disease, while TCR repertoires contract in therapy-resistant patients. Trajectory analysis reveals a continuum of CD8+ T cell phenotypes, characterized by differential expression of granzyme B and a bone marrow-residing memory CD8+ T cell subset, in which a population with stem-like properties expressing granzyme K is enriched in responders. Chromosome 7/7q loss, on the other hand, is a cancer-intrinsic genomic marker of PD-1 blockade resistance in AML. In summary, our study reveals that adaptive T cell plasticity and genomic alterations determine responses to PD-1 blockade in acute myeloid leukemia.

Download Full-text

Altered Spatial Composition of the Immune Cell Repertoire in Association to CD34+ Blasts in Myelodysplastic Syndromes and Secondary Acute Myeloid Leukemia

Cancers ◽

10.3390/cancers13020186 ◽

2021 ◽

Vol 13 (2) ◽

pp. 186

Author(s):

Marcus Bauer ◽

Christoforos Vaxevanis ◽

Haifa Kathrin Al-Ali ◽

Nadja Jaekel ◽

Christin Le Hoa Naumann ◽

...

Keyword(s):

T Cells ◽

Acute Myeloid Leukemia ◽

Myelodysplastic Syndromes ◽

Myeloid Leukemia ◽

Multispectral Imaging ◽

Immune Cell ◽

Genetic Alterations ◽

Spatial Proximity ◽

Secondary Acute Myeloid Leukemia ◽

Acute Myeloid

Background: Myelodysplastic syndromes (MDS) are caused by a stem cell failure and often include a dysfunction of the immune system. However, the relationship between spatial immune cell distribution within the bone marrow (BM), in relation to genetic features and the course of disease has not been analyzed in detail. Methods: Histotopography of immune cell subpopulations and their spatial distribution to CD34+ hematopoietic cells was determined by multispectral imaging (MSI) in 147 BM biopsies (BMB) from patients with MDS, secondary acute myeloid leukemia (sAML), and controls. Results: In MDS and sAML samples, a high inter-tumoral immune cell heterogeneity in spatial proximity to CD34+ blasts was found that was independent of genetic alterations, but correlated to blast counts. In controls, no CD8+ and FOXP3+ T cells and only single MUM1p+ B/plasma cells were detected in an area of ≤10 μm to CD34+ HSPC. Conclusions: CD8+ and FOXP3+ T cells are regularly seen in the 10 μm area around CD34+ blasts in MDS/sAML regardless of the course of the disease but lack in the surrounding of CD34+ HSPC in control samples. In addition, the frequencies of immune cell subsets in MDS and sAML BMB differ when compared to control BMB providing novel insights in immune deregulation.

Download Full-text

The clinical profile, management, and outcome of febrile neutropenia in acute myeloid leukemia from resource constraint settings

Therapeutic Advances in Infectious Disease ◽

10.1177/20499361211036592 ◽

2021 ◽

Vol 8 ◽

pp. 204993612110365

Author(s):

Kundan Mishra ◽

Suman Kumar ◽

Sandeep Ninawe ◽

Rajat Bahl ◽

Ashok Meshram ◽

...

Keyword(s):

Overall Survival ◽

Acute Myeloid Leukemia ◽

Febrile Neutropenia ◽

Burkholderia Cepacia ◽

Myeloid Leukemia ◽

Tertiary Care ◽

Care Hospital ◽

Significant Difference ◽

The Mean ◽

Acute Myeloid

Introduction: Acute myeloid leukemia (AML) is the commonest leukemia in adults. Mortality in thew first 30-days ranges from 6% to 43%, while infections account for 30–66% of early deaths. We aim to present our experience of infections in newly-diagnosed AML. Method: This prospective, observational study, was undertaken at a tertiary care hospital in Northern India. Patients with confirmed AML (bone marrow morphology and flow cytometry) and who had developed febrile neutropenia (FN), were included. Result: A total of fifty-five patients were included in the study. The median age of the patients was 47.1 years (12–71) and 28 (50.9%) were males. Fever (33, 60%) was the commonest presentation at the time of diagnosis. One or more comorbid conditions were present in 20 patients (36.36%). Infection at presentation was detected in 17 patients (30.9%). The mean duration to develop febrile neutropenia since the start of therapy was 11.24 days. With each ten-thousand increase in white blood cell (WBC) count, the mean number of days of FN development decreased by 0.35 days ( p = 0.029). Clinical and/or radiological localization was possible in 23 patients (41.81%). Thirty-four blood samples (34/242, 14.04%) from 26 patients (26/55, 47.3%) isolated one or more organisms. Gram negative bacilli (GNB) were isolated in 24 (70.58%) samples. Burkholderia cepacia (8/34, 23.52%) was the commonest organism. The number of days required to develop febrile neutropenia was inversely associated with overall survival (OS). However, when compared, there was no statistically significant difference in OS between patients developing fever on day-10 and day-25 ( p = 0.063). Thirteen patients (23.63%) died during the study period. Discussion: Low percentage of blood culture positivity and high incidence of MDR organisms are a matter of concern. Days to develop febrile neutropenia were inversely associated with overall survival (OS), emphasizing the importance of preventive measures against infections. Conclusion: Infections continues to be a major cause of morbidity and mortality among AML patients.

Download Full-text

Antileukemic activity of rapamycin in acute myeloid leukemia

Blood ◽

10.1182/blood-2004-06-2494 ◽

2005 ◽

Vol 105 (6) ◽

pp. 2527-2534 ◽

Cited By ~ 207

Author(s):

Christian Récher ◽

Odile Beyne-Rauzy ◽

Cécile Demur ◽

Gaëtan Chicanne ◽

Cédric Dos Santos ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

De Novo ◽

Mammalian Target Of Rapamycin ◽

Cell Types ◽

Mtor Inhibition ◽

Growth And Survival ◽

Clinical Responses ◽

De Novo Aml ◽

Acute Myeloid

AbstractThe mammalian target of rapamycin (mTOR) is a key regulator of growth and survival in many cell types. Its constitutive activation has been involved in the pathogenesis of various cancers. In this study, we show that mTOR inhibition by rapamycin strongly inhibits the growth of the most immature acute myeloid leukemia (AML) cell lines through blockade in G0/G1 phase of the cell cycle. Accordingly, 2 downstream effectors of mTOR, 4E-BP1 and p70S6K, are phosphorylated in a rapamycin-sensitive manner in a series of 23 AML cases. Interestingly, the mTOR inhibitor markedly impairs the clonogenic properties of fresh AML cells while sparing normal hematopoietic progenitors. Moreover, rapamycin induces significant clinical responses in 4 of 9 patients with either refractory/relapsed de novo AML or secondary AML. Overall, our data strongly suggest that mTOR is aberrantly regulated in most AML cells and that rapamycin and analogs, by targeting the clonogenic compartment of the leukemic clone, may be used as new compounds in AML therapy.

Download Full-text

Single Cell Atlas of Human Dura Reveals Cellular Meningeal Landscape and Insights into Meningioma Immune Response

10.1101/2021.08.03.454066 ◽

2021 ◽

Author(s):

Anthony Z Wang ◽

Jay Bowman-Kirigin ◽

Rupen Desai ◽

Pujan Patel ◽

Bhuvic Patel ◽

...

Keyword(s):

Single Cell ◽

Immune Cell ◽

Immune Surveillance ◽

Copy Number Variant ◽

Cell Types ◽

Cell Receptor ◽

Immune Microenvironment ◽

Clinical Models ◽

Insight Into

Recent investigation of the meninges, specifically the dura layer, has highlighted its importance in CNS immune surveillance beyond a purely structural role. However, most of our understanding of the meninges stems from the use of pre-clinical models rather than human samples. In this study, we use single cell RNA-sequencing to perform the first characterization of both non-tumor-associated human dura and meningioma samples. First, we reveal a complex immune microenvironment in human dura that is transcriptionally distinct from that of meningioma. In addition, through T cell receptor sequencing, we show significant TCR overlap between matched dura and meningioma samples. We also identify a functionally heterogeneous population of non-immune cell types and report copy-number variant heterogeneity within our meningioma samples. Our comprehensive investigation of both the immune and non-immune cell landscapes of human dura and meningioma at a single cell resolution provide new insight into previously uncharacterized roles of human dura.

Download Full-text

Human-level recognition of blast cells in acute myeloid leukemia with convolutional neural networks

10.1101/564039 ◽

2019 ◽

Cited By ~ 1

Author(s):

Christian Matek ◽

Simone Schwarz ◽

Karsten Spiekermann ◽

Carsten Marr

Keyword(s):

Acute Myeloid Leukemia ◽

Blood Cells ◽

Myeloid Leukemia ◽

White Blood Cells ◽

Cell Types ◽

Hematologic Malignancies ◽

Malignant Cell ◽

Morphological Examination ◽

Blast Cells ◽

Acute Myeloid

AbstractReliable recognition of malignant white blood cells is a key step in the diagnosis of hematologic malignancies such as Acute Myeloid Leukemia. Microscopic morphological examination of blood cells is usually performed by trained human examiners, making the process tedious, time-consuming and hard to standardise.We compile an annotated image dataset of over 18,000 white blood cells, use it to train a convolutional neural network for leukocyte classification, and evaluate the network’s performance. The network classifies the most important cell types with high accuracy. It also allows us to decide two clinically relevant questions with human-level performance, namely (i) if a given cell has blast character, and (ii) if it belongs to the cell types normally present in non-pathological blood smears.Our approach holds the potential to be used as a classification aid for examining much larger numbers of cells in a smear than can usually be done by a human expert. This will allow clinicians to recognize malignant cell populations with lower prevalence at an earlier stage of the disease.

Download Full-text

Massively parallel quantification of phenotypic heterogeneity in single cell drug responses

10.1101/2020.12.18.423559 ◽

2020 ◽

Cited By ~ 1

Author(s):

Benjamin B. Yellen ◽

Jon S. Zawistowski ◽

Eric A. Czech ◽

Caleb I. Sanford ◽

Elliott D. SoRelle ◽

...

Keyword(s):

Machine Learning ◽

Acute Myeloid Leukemia ◽

Single Cell ◽

Myeloid Leukemia ◽

Single Cell Analysis ◽

Phenotypic Heterogeneity ◽

Massively Parallel ◽

Cell Analysis ◽

On Chip ◽

Acute Myeloid

AbstractSingle cell analysis tools have made significant advances in characterizing genomic heterogeneity, however tools for measuring phenotypic heterogeneity have lagged due to the increased difficulty of handling live biology. Here, we report a single cell phenotyping tool capable of measuring image-based clonal properties at scales approaching 100,000 clones per experiment. These advances are achieved by exploiting a novel flow regime in ladder microfluidic networks that, under appropriate conditions, yield a mathematically perfect cell trap. Machine learning and computer vision tools are used to control the imaging hardware and analyze the cellular phenotypic parameters within these images. Using this platform, we quantified the responses of tens of thousands of single cell-derived acute myeloid leukemia (AML) clones to targeted therapy, identifying rare resistance and morphological phenotypes at frequencies down to 0.05%. This approach can be extended to higher-level cellular architectures such as cell pairs and organoids and on-chip live-cell fluorescence assays.

Download Full-text

An Immune Checkpoint-Related Gene Signature for Predicting Survival of Pediatric Acute Myeloid Leukemia

Journal of Oncology ◽

10.1155/2021/5550116 ◽

2021 ◽

Vol 2021 ◽

pp. 1-14

Author(s):

Feng Jiang ◽

Xin-Yu Wang ◽

Ming-Yan Wang ◽

Yan Mao ◽

Xiao-Lin Miao ◽

...

Keyword(s):

Acute Myeloid Leukemia ◽

Immune Checkpoint ◽

Myeloid Leukemia ◽

Immune Cell ◽

Cox Regression ◽

Secondary Data ◽

Gene Signature ◽

Pediatric Acute Myeloid Leukemia ◽

Pediatric Aml ◽

Acute Myeloid

Objective. The aim of this research was to create a new genetic signature of immune checkpoint-associated genes as a prognostic method for pediatric acute myeloid leukemia (AML). Methods. Transcriptome profiles and clinical follow-up details were obtained in Therapeutically Applicable Research to Generate Effective Treatments (TARGET), a database of pediatric tumors. Secondary data was collected from the Gene Expression Omnibus (GEO) to test the observations. In univariate Cox regression and multivariate Cox regression studies, the expression of immune checkpoint-related genes was studied. A three-mRNA signature was developed for predicting pediatric AML patient survival. Furthermore, the GEO cohort was used to confirm the reliability. A bioinformatics method was utilized to identify the diagnostic and prognostic value. Results. A three-gene (STAT1, BATF, EML4) signature was developed to identify patients into two danger categories depending on their OS. A multivariate regression study showed that the immune checkpoint-related signature (STAT1, BATF, EML4) was an independent indicator of pediatric AML. By immune cell subtypes analyses, the signature was correlated with multiple subtypes of immune cells. Conclusion. In summary, our three-gene signature can be a useful tool to predict the OS in AML patients.

Download Full-text

Genetic Landscape of Mitochondrial Regulatory Region in Pediatric Acute Myeloid Leukemia: Changes from Diagnosis to Relapse

Journal of Pediatric Genetics ◽

10.1055/s-0039-1696976 ◽

2019 ◽

Vol 08 (04) ◽

pp. 193-197

Author(s):

Anudishi Tyagi ◽

Raja Pramanik ◽

Radhika Bakhshi ◽

Sreenivas Vishnubhatla ◽

Sameer Bakhshi

Keyword(s):

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

De Novo ◽

Regulatory Region ◽

Mt Dna ◽

Pediatric Acute Myeloid Leukemia ◽

Loop Region ◽

Significant Difference ◽

D Loop ◽

Acute Myeloid

AbstractThis prospective study aimed to compare the pattern of mitochondrial deoxyribonucleic acid D-loop (mt-DNA D-loop) variations in 41 paired samples of de novo pediatric acute myeloid leukemia (AML) (baseline vs. relapse) patients by Sanger's sequencing. Mean mt-DNA D-loop variation was 10.1 at baseline as compared with 9.4 per patients at relapse. In our study, 28 (68.3%) patients showed change in number of variations from baseline to relapse, 11 (26.8%) patients showed increase, 17 (41.6%) patients showed decrease, and 7 (17.1%) patients who suffered a relapse had a gain at position T489C. No statistically significant difference was observed in the mutation profile of mt-DNA D-loop region from baseline to relapse in the evaluated population of pediatric AML.

Download Full-text