Biology subjects

Safi, F.

Publications and source records attributed to Safi, F..

4 recordsLinked to original sources

bioRxiv2023

CD9 marks myeloid/MegE-biased human hematopoiesis

Rare hematopoietic stem cells make up an infrequent but critical population in the bone marrow (BM), maintaining and replenishing the entire hematopoietic system. Importantly, despite sharing the unique stem cell properties of multilineage differentiation and self-renewal, individual HSCs are functionally heterogeneous, and this heterogeneity increases during aging. While HSCs in young mice are qualitatively more similar, ageing is marked by an increased size of the HSC pool and substantial functional variation of individual HSCs. CD9 is a cell surface marker that is highly expressed in HSCs in mice, while CD9 expression within the human HSC population has been reported to be low during neonatal hematopoiesis. Here, we have investigated CD9 expression levels in the human HSPC population over time and identified that early in life; CD9 is infrequent in HSCs, but marks progenitor populations with low engraftment potential and high proliferation capacity. However, during situations of myeloid/Megakaryocyte-erythoid (MegE) biased hematopoiesis, such as during ageing or in leukemia, there is a substantial increase of CD9 expression in HSPCs. Thus, CD9 represents an HSC marker for myeloid/MegE-biased hematopoiesis.

cell biology↗

bioRxiv2023

Single cell multi-omics analysis of chronic myeloid leukemia links cellular heterogeneity to therapy response

The advent of tyrosine kinase inhibitors (TKIs) as treatment of chronic myeloid leukemia (CML) is a paradigm in molecularly targeted cancer therapy. Nonetheless, TKI insensitive leukemia stem cells (LSCs) persist in most patients even after years of treatment. The sustained presence, heterogeneity and evolvability of LSCs are imperative for disease progression as well as recurrence during treatment-free remission (TFR). However, dynamic changes among LSC sub-populations upon TKI therapy impede their measurement and targeting. Here, we used cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to generate high-resolution single cell multiomics maps from CML patients at diagnosis, retrospectively stratified by BCR::ABL1IS (%) following 12 months of TKI therapy as per European LeukemiaNet (ELN) recommendations. Simultaneous measurement of global gene expression profiles together with >40 surface markers from the same cells revealed that each patient harbored a unique composition of stem and progenitor cells at diagnosis demonstrating that cellular heterogeneity is a hallmark of CML. The patients with treatment failure after 12 months of therapy had markedly higher abundance of molecularly defined primitive cells at diagnosis compared to the optimal responders. Furthermore, deconvolution of an independent dataset of CML patient-derived bulk transcriptomes (n=59) into constituent cell populations showed that the proportion of primitive cells versus lineage primed sub-populations significantly connected with the TKI-treatment outcome. The multiomic feature landscape enabled visualization of the primitive fraction as a heterogenous mixture of molecularly distinct Lin-CD34+CD38-/low BCR::ABL1+ LSCs and BCR::ABL1- hematopoietic stem cells (HSCs) in variable ratio across patients and guided their prospective isolation by a combination of CD26 and CD35 cell surface markers. We for the first time show that BCR::ABL1+ LSCs and BCR::ABL1- HSCs can be distinctly separated as CD26+CD35- and CD26-CD35+ respectively. In addition, we found the relative proportion of CD26-CD35+ HSCs to be higher in optimal responders when compared to treatment failures, at diagnosis as well as following 3 months of TKI therapy, and that the LSC/HSC ratio was increased in patients with prospective treatment failure. Collectively, the patient-specific cellular heterogeneity multiomics maps build a framework towards understanding therapy response and adapting treatment by devising strategies that either extinguish TKI-insensitive LSCs or engage the immune effectors to suppress the residual leukemogenic cells.

cancer biology↗

bioRxiv2021

Single-Cell Multiomics Reveals Distinct Cell States at the Top of Human Hematopoietic Hierarchy

The advent of single cell (Sc) genomics has challenged the dogma of haematopoiesis as a tree-like structure of stepwise lineage commitment through distinct and increasingly restricted progenitor populations. Instead, analysis of ScRNA-seq has proposed that the earliest events in human hematopoietic stem cell (HSC) differentiation are characterized by only subtle molecular changes, with hematopoietic stem and progenitor cells (HSPCs) existing as a continuum of low-primed cell-states that gradually transition into a specific lineage (CLOUD-HSPCs). Here, we combine ScRNA-seq, ScATAC-seq and cell surface proteomics to dissect the heterogeneity of CLOUD-HSPCs at different stages of human life. Within CLOUD-HSPCs, pseudotime ordering of both mRNA and chromatin data revealed a bifurcation of megakaryocyte/erythroid and lympho/myeloid trajectories immediately downstream a subpopulation with an HSC-specific enhancer signature. Importantly, both HSCs and lineage-restricted progenitor populations could be prospectively isolated based on correlation of their molecular signatures with CD35 and CD11A expression, respectively. Moreover, we describe the changes that occur in this heterogeneity as hematopoiesis develops from neonatal to aged bone marrow, including an increase of HSCs and depletion of lympho-myeloid biased MPPs. Thus, this study dissects the heterogeneity of human CLOUD-HSPCs revealing distinct HSPC-states of relevance in homeostatic settings such as ageing.

cell biology↗

bioRxiv2020

Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction

The emerging notion of hematopoietic stem- and progenitor cells (HSPCs) as a low-primed cloud without sharply demarcated gene expression programs raises the question on how cellular fate options emerge, and at which stem-like stage lineage priming is initiated. Here we investigated single-cell chromatin accessibility of Lineage-, cKit+, Sca1+ (LSK) HSPCs spanning the early differentiation landscape. Application of a signal-processing algorithm to detect transition points corresponding to massive alterations in accessibility of 571 transcription factor-motifs revealed a population of LSK FMS-like tyrosine kinase 3(Flt3)intCD9high cells that concurrently display stem-like and lineage-affiliated chromatin signatures pointing to a simultaneous gain of both Lympho-Myeloid and Megakaryocyte-Erythroid programs. Molecularly and functionally, these cells position between stem cells and committed progenitors, display multi-lineage capacity in vitro and in vivo, but lack self-renewal activity. This integrative molecular analysis resolves the heterogeneity of cells along hematopoietic differentiation and permits investigation of chromatin-mediated transition between multipotency and lineage restriction.

cell biology↗