Niche-modulated and niche-modulating genes in bone marrow cells.

Blood Cancer J. 2012 Dec 14;2:e97.

Yossi Cohen1, Osnat Garach-Jehoshua2, Adina Bar-Chaim3 and Abraham Kornberg1

1Department of Hematology, 2Hematology Laboratory and 3Chemistry Department, Assaf Harofeh Medical Center, Zerifin, Israel. Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Israel

Corresponding author:

Dr Yossi Cohen, MD, BsC,
Department of Hematology,
Assaf Harofeh Medical Center,
Zerifin 70300, Israel.
Tel: +972 8 9778223,
Fax: +972 8 9779772


Bone marrow (BM) cells depend on their niche for growth and survival. However, the genes modulated by niche stimuli have not been discriminated yet. For this purpose, we investigated BM aspirations from patients with various hematological malignancies. Each aspirate was fractionated, and the various samples were fixed at different time points and analyzed by microarray. Identification of niche-modulated genes relied on sustained change in expression following loss of niche regulation. Compared with the reference (‘authentic’) samples, which were fixed immediately following aspiration, the BM samples fixed after longer stay out-of-niche acquired numerous changes in gene-expression profile (GEP). The overall genes modulated included a common subset of functionally diverse genes displaying prompt and sustained ‘switch’ in expression irrespective of the tumor type. Interestingly, the ‘switch’ in GEP was reversible and turned ‘off-and-on’ again in culture conditions, resuming cell-cell-matrix contact versus respread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of tumor cells out-of-niche, and the regression of the ‘contactless switch’ was followed by induction of a new set of genes, this time mainly encoding extracellular proteins including angiogenic factors and extracellular matrix proteins. Our data set, being unique in authentic expression design, uncovered niche-modulated and niche-modulating genes capable of controlling homing, expansion and angiogenesis.

PMID: 23241658



Our working hypothesis was that the fatal fate of bone marrow (BM) cells ex-vivo must be preceded by corresponding changes in expression of the genes which were tightly controlled by the BM niche (1). If this holds true, it would be easy to detect in any BM-cell subset the niche controlled genes simply by comparing the gene expression profile (GEP) in BM samples left for a while ex-vivo versus the GEP recorded from control samples which were fixed immediately following aspiration. To overcome the limitation of cell separation which would prevent immediate fixation of the control samples (used to record the GEP “in-vivo”) we selected patients with ~ 100% BM infiltration by tumor cells which eliminated the need for cell separation. As predicted, the GEP comparisons revealed spontaneous evolvement of prompt and sustained switch in the expression of numerous genes following aspiration, among which > 60 genes were reproducible irrespective of the underlying tumor (leukemia, lymphoma or myeloma) or the duration of cell stay ex-vivo (in the range from several minutes to 11 hours). This subset of genes could be subdivided among 4 physiological functions (Figure 1):

1. Homing (e.g. RGS1, CD69)

2. Tumor expansion (e.g. PTGS2, AREG)

3. Stromal expansion/Angiogenesis (e.g. AREG, PTGS2, RGS2, NR4A2, IL8).

 4. Tumor suppression (e.g. JUN, EGR1, KLF4, FOSB, CD69, PPP1R15A, TRIB1). Moreover it was found that most of the GEP changes evolved following aspiration regressed under culture conditions that resume cell-cell-matrix contact in-vitro. In other words, in their free floating state the aspirated BM cells actually express their default GEP which will return to be controlled only after resuming cell-cell contact upon matrix engagement. Interestingly, the regression of the postaspiration changes in GEP under cell-cell-matrix contact in-vitro was followed by increased viability of the tumor cells. However, during culture there was also upregulation of a new set of genes, this time mostly encoding for extracellular proteins (especially angiogenic factors and extracellular matrix proteins) combined with downregulation of a large subset of mitotic genes which could explain the ensuing mitotic arrest (2). In conclusion, our GEP comparisons disclosed a large subset of niche regulated genes which can be subject to various manipulations in order to kill the tumor cells in-vivo or to increase their survival in-vitro.



  1. Cohen Y, Garach-Jehoshua O, Bar-Chaim A, Kornberg A. Niche-modulated and niche-modulating genes in bone marrow cells.  Blood Cancer J. 2012 14;2:e97.
  2. Cohen Y, Gutwein O, Garach-Jehoshua O, Bar-Chaim A, Kornberg A. The proliferation arrest of primary tumor cells out-of-niche is associated with widespread downregulation of mitotic and transcriptional genes. Hematology, 2013, in print.

Yossi Cohen-1

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