Identification of a novel c-DNA overexpressed in Fanconi's anemia fibroblasts partially homologous to a putative L-3-phosphoserine-phosphatase

Transcriptomics and chromatin accessibility in multiple African population samples

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

Race-associated biological differences among luminal A and basal-like breast cancers in the Carolina Breast Cancer Study

BACKGROUND

We examined racial differences in the expression of eight genes and their associations with risk of recurrence among 478 white and 495 black women who participated in the Carolina Breast Cancer Study Phase 3.

METHODS

Breast tumor samples were analyzed for PAM50 subtype and for eight genes previously found to be differentially expressed by race and associated with breast cancer survival: ACOX2, MUC1, FAM177A1, GSTT2, PSPH, PSPHL, SQLE, and TYMS. The expression of these genes according to race was assessed using linear regression and each gene was evaluated in association with recurrence using Cox regression.

RESULTS

Compared to white women, black women had lower expression of MUC1, a suspected good prognosis gene, and higher expression of GSTT2, PSPHL, SQLE, and TYMS, suspected poor prognosis genes, after adjustment for age and PAM50 subtype. High expression (greater than median versus less than or equal to median) of FAM177A1 and PSPH was associated with a 63% increase (hazard ratio (HR) = 1.63, 95% confidence interval (CI) = 1.09-2.46) and 76% increase (HR = 1.76, 95% CI = 1.15-2.68), respectively, in risk of recurrence after adjustment for age, race, PAM50 subtype, and ROR-PT score. Log₂-transformed SQLE expression was associated with a 20% increase (HR = 1.20, 95% CI = 1.03-1.41) in recurrence risk after adjustment. A continuous multi-gene score comprised of eight genes was also associated with increased risk of recurrence among all women (HR = 1.11, 95% CI = 1.04-1.19) and among white (HR = 1.14, 95% CI = 1.03-1.27) and black (HR = 1.11, 95% CI = 1.02-1.20) women.

CONCLUSIONS

Racial differences in gene expression may contribute to the survival disparity observed between black and white women diagnosed with breast cancer.

PSPHL and breast cancer in African American women: causative gene or population stratification?

Background

Phophoserine phosphatase-like (PSPHL) is expressed at significantly higher levels in breast tumors from African American women (AAW) compared to Caucasian women (CW). How overexpression of PSPHL contributes to outcome disparities is unclear, thus, molecular mechanisms driving expression differences between populations were evaluated.

Results

PCR was used to detect deletion of 30-Kb of chromosome 7p11 including the first three exons of PSPHL using genomic DNA from AAW (199 with invasive breast cancer, 360 controls) and CW (invasive breast cancer =589, 364 controls). Gene expression levels were evaluated by qRT-PCR using RNA isolated from tumor tissue and blood. Data were analyzed using chi-square analysis and Mann–Whitney U-tests; P < 0.05 was used to define significance. Gene expression levels correlated with deletion status: patients homozygous for the deletion had no detectable expression of PSPHL, while heterozygous had expression levels 2.1-fold lower than those homozygous for retention of PSPHL. Homozygous deletion of PSPHL was detected in 61% of CW compared to 6% of AAW with invasive breast cancer (P < 0.0001); genotype frequencies did not differ significantly between AAW with and without breast cancer (P = 0.211).

Conclusions

Thus, deletion of 7p11, which prevents expression of PSPHL, is significantly higher in CW compared to AAW, suggesting that this 30-kb deletion and subsequent disruption of PSPHL may be a derived trait in Caucasians. The similar frequency of the deletion allele in AAW with and without invasive breast cancer suggests that this difference represent population stratification, and does not contribute to cancer disparities.

Analysis of PSPHL as a Candidate Gene Influencing the Racial Disparity in Endometrial Cancer

Endometrial cancer is the most commonly diagnosed gynecologic malignancy in the United States. A well recognized disparity by race in both incidence and survival outcome exists for this cancer. Specifically Caucasians are about two times more likely to develop endometrial cancer than are African-Americans. However, African-American women are more likely to die from this disease than are Caucasians. The basis for this disparity remains unknown. Previous studies have identified differences in the types and frequencies of gene mutations among endometrial cancers from Caucasians and African-Americans suggesting that the tumors from these two groups might have differing underlying genetic defects. We performed a gene expression microarray study in an effort to identify differentially expressed transcripts between African-American and Caucasian women's endometrial cancers. Our gene expression screen identified a list of potential biomarkers that are differentially expressed between these two groups of cancers. Of these we identified a poorly characterized transcript with a region of homology to phospho serine phosphatase (PSPH) and designated phospho serine phosphatase like (PSPHL) as the most differentially over-expressed gene in cancers from African-Americans. We further clarified the nature of expressed transcripts. Northern blot analysis confirmed the message was limited to a transcript of under 1 kB. Sequence analysis of transcripts confirmed two alternate open reading frame (ORF) isoforms due to alternative splicing events. Splice specific primer sets confirmed both isoforms were differentially expressed in tissues from Caucasians and African-Americans. We further examined the expression in other tissues from women to include normal endometrium, normal and malignant ovary. In all cases PSPHL expression was more often present in tissues from African-Americans than Caucasians. Our data confirm the African-American based expression of the PSPHL transcript in endometrial cancer and also identify its expression in other tissues from African-Americans including ovary and ovarian cancer. PSPHL represents a candidate gene that might influence the observed racial disparity in endometrial and other cancers.

Identification of differentially expressed genes in breast tumors from African American compared with Caucasian women

BACKGROUND

Breast tumors from African American women have less favorable pathological characteristics and higher mortality rates than those of Caucasian women. Although socioeconomic status may influence prognosis, biological factors are also likely to contribute to tumor behavior.

METHODS

Patients with invasive breast cancer were matched by age, grade, and estrogen receptor status; patients with benign disease were matched by age and diagnosis type. RNA from laser microdissected tumors and whole-sectioned nonmalignant breast tissues was hybridized to HG U133A 2.0 microarrays. Data were analyzed using Partek Genomics Suite using a cutoff of P < .001, >1.5-fold change, and results were validated by quantitative real-time polymerase chain reaction.

RESULTS

Clinicopathological factors did not differ significantly between groups for age at diagnosis, tumor size or stage, lymph node or human epidermal growth receptor 2 status, intrinsic subtype, or mortality. Two-way analysis of the tumor specimens revealed 25 probes representing 23 genes differentially expressed between populations; hierarchical clustering classified 24 of 26 African American women and 25 of 26 Caucasian women correctly. In the nonmalignant specimens, 15 probes representing 13 genes were differentially expressed, including 5 genes that also differed in the tumor specimens; these genes were able to correctly classify nonmalignant breast specimens from 20 of 22 of African American women and all of the Caucasian women.

CONCLUSIONS

Despite matching of tumors by pathological characteristics, molecular profiles differed between African American women and Caucasian women in both invasive tumors and benign breast tissues. These differentially expressed genes, including CRYBB2, PSPHL, and SOS1, are involved in cellular growth and differentiation, invasion, metastasis, and immune response and thus may contribute to the poor outcome in African American women.

Differential endothelial cell gene expression by African Americans versus Caucasian Americans: a possible contribution to health disparity in vascular disease and cancer

BACKGROUND

Health disparities and the high prevalence of cardiovascular disease continue to be perplexing worldwide health challenges. This study addresses the possibility that genetic differences affecting the biology of the vascular endothelium could be a factor contributing to the increased burden of cardiovascular disease and cancer among African Americans (AA) compared to Caucasian Americans (CA).

METHODS

From self-identified, healthy, 20 to 29-year-old AA (n = 21) and CA (n = 17), we established cultures of blood outgrowth endothelial cells (BOEC) and applied microarray profiling. BOEC have never been exposed to in vivo influences, and their gene expression reflects culture conditions (meticulously controlled) and donor genetics. Significance Analysis of Microarray identified differential expression of single genes. Gene Set Enrichment Analysis examined expression of pre-determined gene sets that survey nine biological systems relevant to endothelial biology.

RESULTS

At the highly stringent threshold of False Discovery Rate (FDR) = 0, 31 single genes were differentially expressed in AA. PSPH exhibited the greatest fold-change (AA > CA), but this was entirely accounted for by a homolog (PSPHL) hidden within the PSPH probe set. Among other significantly different genes were: for AA > CA, SOS1, AMFR, FGFR3; and for AA < CA, ARVCF, BIN3, EIF4B. Many more (221 transcripts for 204 genes) were differentially expressed at the less stringent threshold of FDR <.05. Using the biological systems approach, we identified shear response biology as being significantly different for AA versus CA, showing an apparent tonic increase of expression (AA > CA) for 46/157 genes within that system.

CONCLUSIONS

Many of the genes implicated here have substantial roles in endothelial biology. Shear stress response, a critical regulator of endothelial function and vascular homeostasis, may be different between AA and CA. These results potentially have direct implications for the role of endothelial cells in vascular disease (hypertension, stroke) and cancer (via angiogenesis). Also, they are consistent with our over-arching hypothesis that genetic influences stemming from ancestral continent-of-origin could impact upon endothelial cell biology and thereby contribute to disparity of vascular-related disease burden among AA. The method used here could be productively employed to bridge the gap between information from structural genomics (for example, disease association) and cell function and pathophysiology.

Erythropoiesis: Current Clinical Practice: Advances in the Genetics and Biology of Fanconi Anaemia

The autosomal recessive disorder Fanconi anaemia (FA) has been the subject of intense study for over a decade. The genes mutated in FA patients are being cloned, but so far, the sequences of these genes have not given any clear indication of their function. Various models for the function of the FA proteins have been postulated to explain the spontaneous chromosomal abnormalities and clastogen sensitivity described in FA cells. This review summarises the critical experimental evidence for and against these models, and attempts to give some indication of the possible mechanisms by which mutations in FA genes cause patients to suffer pancytopaenia and acute myeloid leukaemia, as well as an increased risk of other malignancies.

Expression of l-3-phosphoserine phosphatase is regulated by reconstituted basement membrane

Reconstituted basement membrane (Matrigel) promotes differentiation of endometrial adenocarcinoma cells in vitro. However, little is known about the molecular basis of these in vitro differentiation processes. Using differential display RT-PCR to search for potential molecular markers we screened for genes which respond to contact to basement membrane by alteration of expression levels. Here we report that the cDNA MT32 represents an mRNA with a time dependent biphasic response pattern to contact to basement membrane. Characterizing MT32 revealed that the sequence of MT32 is identical to l-3-phosphoserine phosphatase. PCR analysis of l-3-phosphoserine phosphatase expression surprisingly revealed at least three variants of this enzyme. In summary, and in view of the literature, l-3-phosphoserine phosphatase and potential variants or family members represent molecular markers to study regulation of gene expression by components of the extracellular matrix. In conclusion, l-3-phosphoserine phosphatase(s) may be important in endometrial carcinogenesis since this enzyme synthesizes important metabolic intermediates which serve both as building blocks for peptide synthesis and for signal transducing molecules.