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| Status |
Public on Aug 15, 2009 |
| Title |
Gene expression data from CD44+/CD24- cells sorted by flow cytometry |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Tumorigenic breast cancer cells characterized by CD44 expression and low or undetectable CD24 levels (CD44+/CD24-/low) may be resistant to chemotherapy and therefore responsible for cancer relapse. Paired breast cancer core biopsies before and after neoadjuvant chemotherapy or lapatinib were obtained and as single cell suspensions stained using antibodies against CD24, CD44, and lineage markers, and then analyzed by flow cytometry. Mammosphere (MS) formation in culture was compared before and after treatment. Global gene expression differences between cancer cells bearing CD44+/CD24-/low cells and all other sorted cells, and between cancer MS and the primary bulk invasive cancers were analyzed. We report that CD44+/CD24-/low tumorigenic breast cancer cells were intrinsically chemoresistant ─ chemotherapy led to increased CD44+/CD24-/low cells, increased self-renewal capacity on MS assays, and enhanced tumorigeneicity in immunocompromised SCID/Beige mice. Conversely, in patients with HER2 overexpressing tumors, the EGFR/HER2 tyrosine kinase inhibitor, lapatinib decreased CD44+/CD24-/low cells, with the majority of these patients after conventional therapy achieving pathologic complete response, a validated surrogate marker for long-term survival. Gene transcription pathways that underlie chemoresistant, MS-forming CD44+/CD24-/low cells involve genes belonging to stem cell self-renewal, Wnt signaling, and early development pathways.
Keywords: two group comparison
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| Overall design |
Human breast tumor samples were sorted using flow cytometry to select for cells that were CD44+ and CD24-. Gene expression profiles of these cells were compared with profiles of the other sorted cells (CD24+ and CD44-/CD24-).
Core biopsies of primary breast tumors were taken and placed immediately in cold RPMI-1640 supplemented with 10% heat-inactivated newborn calf serum (HINCS, Invitrogen, Carlsbad, CA). Within an hour, the samples were minced and then digested in 10-15 mL of MEGM with 250-300 units/mL collagenase at 370C. The samples were filtered, washed, and then subjected to hypotonic shock to lyse red blood cells. About 106 single cells were re-suspended, incubated for 15 min at 40C with anti-CD44 (APC), anti-CD24 (FITC), and anti-lineage cocktail antibodies (PE-conjugated anti-CD2, CD3, CD10, CD16, CD18, CD31 and CD 140B) (Pharmingen, San Diego, CA) using the manufacturer’s suggested concentrations. The cells were then washed twice, re-suspended with the viability dye propidium iodide, and analyzed using Dako MoFlo flow cytometry. Side- and forward- scatter were used to eliminate debris and cell doublets, and the Lin- cells were further analyzed by CD44 and CD24 markers.
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| Contributor(s) |
Creighton C, Lewis M, Chang J |
| Citation(s) |
19666588 |
| Submission date |
Apr 13, 2007 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Chad Creighton |
| E-mail(s) |
creighto@bcm.tmc.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Biostatistics, Ducan Cancer Center
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| Street address |
One Baylor Plaza, Mail Stop: BCM305
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (29)
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| GSM194580 |
CD44+/CD24- flow sorted cells, biological rep1 |
| GSM194581 |
CD44+/CD24- flow sorted cells, biological rep2 |
| GSM194583 |
CD44+/CD24- flow sorted cells, biological rep3 |
| GSM194584 |
CD44+/CD24- flow sorted cells, biological rep4 |
| GSM194585 |
CD44+/CD24- flow sorted cells, biological rep5 |
| GSM194586 |
CD44+/CD24- flow sorted cells, biological rep6 |
| GSM194587 |
CD44+/CD24- flow sorted cells, biological rep7 |
| GSM194589 |
CD44+/CD24- flow sorted cells, biological rep8 |
| GSM194590 |
CD44+/CD24- flow sorted cells, biological rep9 |
| GSM194592 |
non-CD44+/CD24- flow sorted cells, biological rep1 |
| GSM194593 |
non-CD44+/CD24- flow sorted cells, biological rep2 |
| GSM194594 |
non-CD44+/CD24- flow sorted cells, biological rep3 |
| GSM194596 |
non-CD44+/CD24- flow sorted cells, biological rep4 |
| GSM194597 |
non-CD44+/CD24- flow sorted cells, biological rep5 |
| GSM194598 |
non-CD44+/CD24- flow sorted cells, biological rep6 |
| GSM194600 |
non-CD44+/CD24- flow sorted cells, biological rep7 |
| GSM194601 |
non-CD44+/CD24- flow sorted cells, biological rep8 |
| GSM194602 |
non-CD44+/CD24- flow sorted cells, biological rep9 |
| GSM194603 |
non-CD44+/CD24- flow sorted cells, biological rep10 |
| GSM194604 |
CD44+/CD24- flow sorted cells, biological rep10 |
| GSM194605 |
CD44+/CD24- flow sorted cells, biological rep11 |
| GSM194606 |
CD44+/CD24- flow sorted cells, biological rep12 |
| GSM194607 |
CD44+/CD24- flow sorted cells, biological rep13 |
| GSM194608 |
CD44+/CD24- flow sorted cells, biological rep14 |
| GSM194610 |
non-CD44+/CD24- flow sorted cells, biological rep11 |
| GSM194613 |
non-CD44+/CD24- flow sorted cells, biological rep12 |
| GSM194614 |
non-CD44+/CD24- flow sorted cells, biological rep13 |
| GSM194615 |
non-CD44+/CD24- flow sorted cells, biological rep14 |
| GSM194616 |
non-CD44+/CD24- flow sorted cells, biological rep15 |
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| Relations |
| BioProject |
PRJNA100463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE7513_RAW.tar |
223.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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