Comparative Study of Organoids from Patient-Derived Normal and Tumor Colon and Rectal Tissue

Colon and rectal tumors, often referred to as colorectal cancer, show different gene expression patterns in studies that analyze whole tissue biopsies containing a mix of tumor and non-tumor cells. To better characterize colon and rectal tumors, we investigated the gene expression profile of organoids generated from endoscopic biopsies of rectal tumors and adjacent normal colon and rectum mucosa from therapy-naive rectal cancer patients. We also studied the effect of vitamin D on these organoid types. Gene profiling was performed by RNA-sequencing. Organoids from a normal colon and rectum had a shared gene expression profile that profoundly differed from that of rectal tumor organoids. We identified a group of genes of the biosynthetic machinery as rectal tumor organoid-specific, including those encoding the RNA polymerase II subunits POLR2H and POLR2J. The active vitamin D metabolite 1α,25-dihydroxyvitamin D3/calcitriol upregulated stemness-related genes (LGR5, LRIG1, SMOC2, and MSI1) in normal rectum organoids, while it downregulated differentiation marker genes (TFF2 and MUC2). Normal colon and rectum organoids share similar gene expression patterns and respond similarly to calcitriol. Rectal tumor organoids display distinct and heterogeneous gene expression profiles, with differences with respect to those of colon tumor organoids, and respond differently to calcitriol than normal rectum organoids.

Download Full-text

Early life vitamin D deficiency programs hypothalamic and pituitary dysfunction and alters gene expression patterns

Fertility and Sterility ◽

10.1016/j.fertnstert.2013.07.161 ◽

2013 ◽

Vol 100 (3) ◽

pp. S12

Author(s):

T.E. Fisher ◽

F. Meng ◽

J. Davis ◽

G. Neal-Perry

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Vitamin D Deficiency ◽

Early Life ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Pituitary Dysfunction

Download Full-text

Vitamin D Growth Inhibition of Breast Cancer Cells: Gene Expression Patterns Assessed by cDNA Microarray

Breast Cancer Research and Treatment ◽

10.1023/a:1024487118457 ◽

2003 ◽

Vol 80 (1) ◽

pp. 49-62 ◽

Cited By ~ 121

Author(s):

Srilatha Swami ◽

Nalini Raghavachari ◽

Uwe R. Muller ◽

Yijia P. Bao ◽

David Feldman

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Vitamin D ◽

Growth Inhibition ◽

Cancer Cells ◽

Cdna Microarray ◽

Breast Cancer Cells ◽

Expression Patterns ◽

Gene Expression Patterns

Download Full-text

Parallels between Global Transcriptional Programs of Polarizing Caco-2 Intestinal Epithelial Cells In Vitro and Gene Expression Programs in Normal Colon and Colon Cancer

Molecular Biology of the Cell ◽

10.1091/mbc.e07-04-0309 ◽

2007 ◽

Vol 18 (11) ◽

pp. 4245-4260 ◽

Cited By ~ 85

Author(s):

Annika M. Sääf ◽

Jennifer M. Halbleib ◽

Xin Chen ◽

Siu Tsan Yuen ◽

Suet Yi Leung ◽

...

Keyword(s):

Gene Expression ◽

Colon Cancer ◽

Intestinal Epithelial Cells ◽

Expression Patterns ◽

Human Colon ◽

Gene Expression Patterns ◽

Intestinal Epithelial ◽

Normal Colon ◽

Enterocyte Differentiation

Posttranslational mechanisms are implicated in the development of epithelial cell polarity, but little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized temporal patterns of gene expression during cell–cell adhesion-initiated polarization of cultured human Caco-2 cells, which develop structural and functional polarity resembling enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts. Comparison to gene expression patterns in normal human colon and colon tumors revealed that the pattern in proliferating, nonpolarized Caco-2 cells paralleled patterns seen in human colon cancer in vivo, including expression of genes involved in cell proliferation. The pattern switched in polarized Caco-2 cells to one more closely resembling that in normal colon tissue, indicating that regulation of transcription underlying Caco-2 cell polarization is similar to that during enterocyte differentiation in vivo. Surprisingly, the temporal program of gene expression in polarizing Caco-2 cells involved changes in signaling pathways (e.g., Wnt, Hh, BMP, FGF) in patterns similar to those during migration and differentiation of intestinal epithelial cells in vivo, despite the absence of morphogen gradients and interactions with stromal cells characteristic of enterocyte differentiation in situ. The full data set is available at http://microarray-pubs.stanford.edu/CACO2 .

Download Full-text

Oral Vitamin D supplementation induces transcriptomic changes in rectal mucosa that are consistent with anti-tumour effects.

10.1101/2021.05.04.21255629 ◽

2021 ◽

Author(s):

Peter G Vaughan-Shaw ◽

Graeme Grimes ◽

James P Blackmur ◽

Maria Timofeeva ◽

Marion Walker ◽

...

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Expression Patterns ◽

Rectal Mucosa ◽

Vitamin D Supplementation ◽

Gene Expression Patterns ◽

Blood Biomarkers ◽

Oral Vitamin ◽

Gene Set ◽

Transcriptomic Changes

Background Risk for several common cancers is influenced by the transcriptomic landscape of the respective tissue-of-origin. Vitamin D influences in-vitro gene expression and cancer cell growth. We sought to determine whether oral vitamin D induces beneficial gene expression effects in human rectal epithelium and identify biomarkers of response. Methods Blood and rectal mucosa was sampled from 191 human subjects and mucosa gene expression (HT12) correlated with plasma vitamin D (25-OHD) to identify differentially expressed genes. Fifty subjects were then administered 3200IU/day oral vitamin D3 and matched blood/mucosa resampled after 12 weeks. Transcriptomic changes (HT12/RNAseq) after supplementation were tested against the prioritised genes for gene-set and GO-process enrichment. To identify blood biomarkers of mucosal response, we derived receiver-operator curves and C-statistic (AUC) and tested biomarker reproducibility in an independent Supplementation Trial (BEST-D). Results 629 genes were associated with 25-OHD level (P<0.01), highlighting 453 GO-term processes (FDR<0.05). In the whole intervention cohort, vitamin D supplementation enriched the prioritised mucosal gene-set (upregulated gene-set P<1.0E-07; downregulated gene-set P<2.6E-05) and corresponding GO terms (P=2.90E-02), highlighting gene expression patterns consistent with anti-tumour effects. However, only 9 individual participants (18%) showed a significant response (NM gene-set enrichment P<0.001) to supplementation. Expression changes in HIPK2 and PPP1CC expression served as blood biomarkers of mucosal transcriptomic response (AUC=0.84 [95%CI:0.66-1.00]), and replicated in BEST-D trial subjects (HIPK2 AUC=0.83 [95%CI:0.77-0.89]; PPP1CC AUC=0.91 [95%CI:0.86-0.95]). Conclusions Higher plasma 25-OHD correlates with rectal mucosa gene expression patterns consistent with anti-tumour effects and this beneficial signature is induced by short-term vitamin D supplementation. Heterogenous gene expression responses to vitamin D may limit the ability of randomised trials to identify beneficial effects of supplementation on CRC risk. However, in the current study blood expression changes in HIPK2 and PPP1CC identify those participants with significant anti-tumor transcriptomic responses to supplementation in the rectum. These data provide compelling rationale for a trial of vitamin D and CRC prevention using easily assayed blood gene expression signatures as intermediate biomarkers of response.

Download Full-text

Gene expression analysis suggests that 1,25-dihydroxyvitamin D3reverses experimental autoimmune encephalomyelitis by stimulating inflammatory cell apoptosis

Physiological Genomics ◽

10.1152/physiolgenomics.00003.2004 ◽

2004 ◽

Vol 18 (2) ◽

pp. 141-151 ◽

Cited By ~ 77

Author(s):

Karen M. Spach ◽

Laura B. Pedersen ◽

Faye E. Nashold ◽

Tsuyoshi Kayo ◽

Brian S. Yandell ◽

...

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Experimental Autoimmune Encephalomyelitis ◽

Expression Patterns ◽

Initiation Factor ◽

Terminal Deoxynucleotidyl Transferase ◽

Gene Expression Patterns ◽

Autoimmune Encephalomyelitis ◽

Biological Studies ◽

Experimental Autoimmune

Multiple sclerosis (MS) is a debilitating autoimmune disease of the central nervous system (CNS) that develops in genetically susceptible individuals who are exposed to undefined environmental risk factors. Epidemiological, genetic, and biological evidence suggests that insufficient vitamin D may be an MS risk factor. However, little is known about how vitamin D might be protective in MS. We hypothesized that 1,25-dihydroxyvitamin D3[1,25-(OH)2D3] might regulate gene expression patterns in a manner that would resolve inflammation. To test this hypothesis, experimental autoimmune encephalomyelitis (EAE) was induced in mice, 1,25-(OH)2D3or a placebo was administered, and 6 h later, DNA microarray hybridization was performed with spinal cord RNA to analyze the gene expression patterns. At this time, clinical, histopathological, and biological studies showed that the two groups did not differ in EAE disease, but changes in several 1,25-(OH)2D3-responsive genes indicated that the 1,25-(OH)2D3had reached the CNS. Compared with normal mice, placebo-treated mice with EAE showed increased expression of many immune system genes, confirming the acute inflammation. When 1,25-(OH)2D3was administered, several genes like glial fibrillary acidic protein and eukaryotic initiation factor 2α kinase 4, whose expression increased or decreased with EAE, returned to homeostatic levels. Also, two genes with pro-apoptotic functions, calpain-2 and caspase-8-associated protein, increased significantly. A terminal deoxynucleotidyl transferase-mediated dUTP nicked end labeling study detected increased nuclear fragmentation in the 1,25-(OH)2D3-treated samples, confirming increased apoptosis. Together, these results suggest that sensitization of inflammatory cells to apoptotic signals may be one mechanism by which the 1,25-(OH)2D3resolved EAE.

Download Full-text

Developmental vitamin D 3 deficiency differentially affects ovarian gene expression patterns in adult female mice

Fertility and Sterility ◽

10.1016/j.fertnstert.2012.07.118 ◽

2012 ◽

Vol 98 (3) ◽

pp. S32 ◽

Cited By ~ 3

Author(s):

J.B. Davis ◽

Z. Merhi ◽

B. Tolga-Suntay ◽

G. Neal-Perry

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Adult Female ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Female Mice ◽

Vitamin D 3

Download Full-text

Oral vitamin D supplementation induces transcriptomic changes in rectal mucosa that are linked to anti-tumour effects

BMC Medicine ◽

10.1186/s12916-021-02044-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

P. G. Vaughan-Shaw ◽

G. Grimes ◽

J. P. Blackmur ◽

M. Timofeeva ◽

M. Walker ◽

...

Keyword(s):

Gene Expression ◽

Vitamin D ◽

Expression Patterns ◽

Rectal Mucosa ◽

Vitamin D Supplementation ◽

Gene Expression Patterns ◽

Blood Biomarkers ◽

Oral Vitamin ◽

Gene Set ◽

Transcriptomic Changes

Abstract Background The risk for several common cancers is influenced by the transcriptomic landscape of the respective tissue-of-origin. Vitamin D influences in vitro gene expression and cancer cell growth. We sought to determine whether oral vitamin D induces beneficial gene expression effects in human rectal epithelium and identify biomarkers of response. Methods Blood and rectal mucosa was sampled from 191 human subjects and mucosa gene expression (HT12) correlated with plasma vitamin D (25-OHD) to identify differentially expressed genes. Fifty subjects were then administered 3200IU/day oral vitamin D3 and matched blood/mucosa resampled after 12 weeks. Transcriptomic changes (HT12/RNAseq) after supplementation were tested against the prioritised genes for gene-set and GO-process enrichment. To identify blood biomarkers of mucosal response, we derived receiver-operator curves and C-statistic (AUC) and tested biomarker reproducibility in an independent Supplementation Trial (BEST-D). Results Six hundred twenty-nine genes were associated with 25-OHD level (P < 0.01), highlighting 453 GO-term processes (FDR<0.05). In the whole intervention cohort, vitamin D supplementation enriched the prioritised mucosal gene-set (upregulated gene-set P < 1.0E−07; downregulated gene-set P < 2.6E−05) and corresponding GO terms (P = 2.90E−02), highlighting gene expression patterns consistent with anti-tumour effects. However, only 9 individual participants (18%) showed a significant response (NM gene-set enrichment P < 0.001) to supplementation. Expression changes in HIPK2 and PPP1CC expression served as blood biomarkers of mucosal transcriptomic response (AUC=0.84 [95%CI 0.66–1.00]) and replicated in BEST-D trial subjects (HIPK2 AUC=0.83 [95%CI 0.77–0.89]; PPP1CC AUC=0.91 [95%CI 0.86–0.95]). Conclusions Higher plasma 25-OHD correlates with rectal mucosa gene expression patterns consistent with anti-tumour effects, and this beneficial signature is induced by short-term vitamin D supplementation. Heterogenous gene expression responses to vitamin D may limit the ability of randomised trials to identify beneficial effects of supplementation on CRC risk. However, in the current study blood expression changes in HIPK2 and PPP1CC identify those participants with significant anti-tumour transcriptomic responses to supplementation in the rectum. These data provide compelling rationale for a trial of vitamin D and CRC prevention using easily assayed blood gene expression signatures as intermediate biomarkers of response.

Download Full-text