SACNAS HER_LAB_POSTER- 2nd DRAFT2

1
Finding a Genetic Link Among Women with Triple Negative Breast Cancer Nuria Astrid Perez Varela and Leticia Márquez-Magaña, PhD lth Equity Research Lab, Department of Biology, San Francisco State Univers ABSTRACT EXPERIMENTAL DESIGN Acknowledgements EXPECTED RESULTS FIGURE 1: African American and Latina women have the highest incidence of TNBC in the United States. We expect that all, or more than expected by random probability, of the TNBC samples that are studied will have genetic ancestry that is African. Expected Ancestral Lineage of TNBC Patients Funding for this pilot comes from the California State University Program for Education and Research in Biotechnology (CSUPERB) Entrepreneurial Joint Venture Program. Ms. Perez-Varela was also supported by an NSF REU fellowship from SF State University. We thank Mr. Angel Ku for help in technical aspects of the project, and for continuing with the work. • Amplify, sequence, and determine mtDNA type of remaining samples. • Determining the genetic ancestry of women inform future efforts to develop molecular diagnostic tools and begin to unravel the genetics of TNBC. The specific objective of the pilot study is to identify the mtDNA type of 100 latina women with and without triple-negative breast cancer to determine if an ancestral link exists among patients diagnosed with this form of cancer. OBJECTIVE 100 DNA samples collected from Latinas with and without TNBC were obtained from University of California, San Francisco. - 31 with TNBC - 34 with Triple positive BC - 35 Healthy controls Latinas were used for this study because they are a heterogeneous, admixed population group comprised of African, European, and Native American ancestries. Samples collected from Latinas with TNBC were matched to samples obtained from women with Triple positive breast cancer, and to healthy controls according to age, and reported self and parental origin as in the following table. FIGURE 6: mtDNA ancestry of TNBC samples from U.S. populations are expected to be from the L1, L2 or L3 population groups (African Ancestry) Human Migration and TNBC Rates FIGURE 2: Limited studies of global TNBC distribution suggest African ancestry for women afflicted with this disease. Triple negative breast cancers (TNBC) are characterized by the absence of estrogen receptor, progesterone receptor, and HER-2 expression making them especially deadly. This is because these receptors are the targets for highly successful treatments for breast cancer, and their absence makes it difficult to treat TNBC. TNBC is found in 15% of U.S. women with breast cancer,with African- American women having the highest incidence (Figure 1). In sub-Saharan Africa the rate of TNBC appears to be much higher. A recent study of 75 breast cancer patients in Ghana found that 82% had TNBC. The high rates of TNBC in African American and Ghanaian women suggest it may have a genetic ancestral component. The purpose of this study is to determine the mtDNA type of 100 Latinas with and without TNBC to determine if an ancestral link exists among patients diagnosed with this form of cancer. Latinas are a heterogeneous human sub- population having European, Native American, and African ancestry. The ancestral nature of their maternal lineage can be determined by mtDNA typing. Therefore the mtDNA type of 31 latinas with TNBC, 34 with triple positive breast cancer, and 35 unaffected controls will be determined. Preliminary results show that a TNBC cell line has a mtDNA type indicative of African ancestry; whereas, a triple- positive cell line has a mtDNA type indicative of European ancestry. Consequently, we predict that TNBC samples will display greater percentage of African ancestry. The identification of an ancestral link among women with TNBC may allow for development of methods for its early detection and treatment. Human (maternal) ancestry was identified by mtDNA typing. Specifically, the mtDNA region known as the Hypervariable Region 1 (HVR1), that contains 440 base pairs, was amplified and sequenced to identify the genetic ancestry of Latinas with and without TNBC. Age (years) Self origin Mother's origin Father's origin Cancer status 48 El Salvador El Salvador El Salvador Triple negative 49 El Salvador El Salvador El Salvador Triple positive 50 El Salvador El Salvador El Salvador Healthy FIGURE 3: Latinas are a heterogeneous sub- population Ladder HVR 1 BP 1000 440 100 ladder(-) + + P P P H H H FIGURE 4: HVR-1 Region FIGURE 5: Agarose gel electrophoresis of first six amplifications of mtDNA. Sample # SNPs (C16223T indicates substitution of C at position 16223 in reference sequence with T in sample analyzed) Haplogrou p (mtDNA type) Cancer Status P14 C16223T A16235G C16278T C16294T A16309G L2 Triple positive P22 16111T 16129A 16185G 16223T 16234T 16290T 16319G 16363C A Triple positive P24 T16032G A16151C A16154C A16170C A16191T A16249C C16323T C16378T T16411C H Triple positive RESULTS HVR-1 sequence was confirmed for three samples, and single nucleotide polymorphisms (SNPs) were identified using Chromas Lite. The identified SNPs were used to determine the mtDNA type (haplogroup) using The Genographic Project, Haplogroup Prediction Tool. The amplified and sequenced HVR-1 region of each sample was compared to the Cambridge Reference Sequence (CRS), the first mitochondrial DNA sequence published in 1987 and belonging to haplogroup H. This is a mtDNA type prevalent in European populations. FUTURE DIRECTIONS AND IMPACT OF WORK REFERENCES Carey LA, Perou CM, Livasy CA, Dressler LG, Cowan D, Conway K, Karaca G, Troester MA, Tse CK, Edmiston S, Deming SL, Geradts J, Cheang MC, Nielsen TO, Moorman PG, Earp HS, Millikan RC. Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA. 2006 Jun 7;295(21):2492-502. Stark A, Kleer CG, Martin I, Awuah B, Nsiah-Asare A, Takyi V, Braman M, Quayson SE, Zarbo R, Wicha M, Newman L. African ancestry and higher prevalence of triple-negative breast cancer: findings from an international study. Cancer. 2010 Nov 1;116(21):4926-32. http://4.bp.blogspot.com/_K7q0QX9ib3s/ TSXNAMF-xUI/AAAAAAAAD6U/EnptP8gh2x4/s1600/ mixed.jpg http://64.40.115.138/file/lu/6/52235/ NTIyMzV9K3szNDIwOTI=.jpg?download=1

Transcript of SACNAS HER_LAB_POSTER- 2nd DRAFT2

Page 1: SACNAS HER_LAB_POSTER- 2nd DRAFT2

Finding a Genetic Link Among Women with Triple Negative Breast Cancer

Nuria Astrid Perez Varela and Leticia Márquez-Magaña, PhDHealth Equity Research Lab, Department of Biology, San Francisco State University

ABSTRACT

EXPERIMENTAL DESIGN

Acknowledgements

EXPECTED RESULTS

FIGURE 1: African American and Latina women have the highest incidence of TNBC in the United States.

We expect that all, or more than expected by random probability, of the TNBC samples that are studied will have genetic ancestry that is African.

Expected Ancestral Lineage of TNBC Patients

Funding for this pilot comes from the California State University Program for Education and Research in Biotechnology (CSUPERB) Entrepreneurial Joint Venture Program. Ms. Perez-Varela was also supported by an NSF REU fellowship from SF State University.

We thank Mr. Angel Ku for help in technical aspects of the project, and for continuing with the work.

• Amplify, sequence, and determine mtDNA type of remaining samples.• Determining the genetic ancestry of women inform future efforts to develop molecular diagnostic tools and begin to unravel the genetics of TNBC.

The specific objective of the pilot study is to identify the mtDNA type of 100 latina women with and without triple-negative breast cancer to determine if an ancestral link exists among patients diagnosed with this form of cancer.

OBJECTIVE

100 DNA samples collected from Latinas with and without TNBC were obtained from University of California, San Francisco.

- 31 with TNBC - 34 with Triple positive BC - 35 Healthy controls

Latinas were used for this study becausethey are a heterogeneous, admixed population group comprised of African,European, and Native American ancestries.

Samples collected from Latinas with TNBC were matched to samples obtained from women with Triple positive breast cancer, and to healthy controls according to age, and reported self and parental origin as in the following table.

FIGURE 6: mtDNA ancestry of TNBC samples from U.S. populations are expected to be from the L1, L2 or L3 population groups (African Ancestry)

Human Migration and TNBC Rates

FIGURE 2: Limited studies of global TNBC distribution suggest African ancestry for women afflicted with this disease.

Triple negative breast cancers (TNBC) are characterized by the absence of estrogen receptor, progesterone receptor, and HER-2 expression making them especially deadly. This is because these receptors are the targets for highly successful treatments for breast cancer, and their absence makes it difficult to treat TNBC. TNBC is found in 15% of U.S. women with breast cancer,with African-American women having the highest incidence (Figure 1). In sub-Saharan Africa the rate of TNBC appears to be much higher. A recent study of 75 breast cancer patients in Ghana found that 82% had TNBC. The high rates of TNBC in African American and Ghanaian women suggest it may have a genetic ancestral component. The purpose of this study is to determine the mtDNA type of 100 Latinas with and without TNBC to determine if an ancestral link exists among patients diagnosed with this form of cancer. Latinas are a heterogeneous human sub-population having European, Native American, and African ancestry. The ancestral nature of their maternal lineage can be determined by mtDNA typing. Therefore the mtDNA type of 31 latinas with TNBC, 34 with triple positive breast cancer, and 35 unaffected controls will be determined. Preliminary results show that a TNBC cell line has a mtDNA type indicative of African ancestry; whereas, a triple-positive cell line has a mtDNA type indicative of European ancestry. Consequently, we predict that TNBC samples will display greater percentage of African ancestry. The identification of an ancestral link among women with TNBC may allow for development of methods for its early detection and treatment.

Human (maternal) ancestry was identified by mtDNA typing. Specifically, the mtDNA region known as the Hypervariable Region 1 (HVR1), that contains 440 base pairs, was amplified and sequenced to identify the genetic ancestry of Latinas with and without TNBC.

Age (years) Self origin Mother's origin Father's origin Cancer status

48 El Salvador El Salvador El Salvador Triple negative

49 El Salvador El Salvador El Salvador Triple positive

50 El Salvador El Salvador El Salvador Healthy

FIGURE 3: Latinas are a heterogeneous sub-population

Ladder HVR 1BP

1000

440

100

ladder (-) + + P P P H H H

FIGURE 4: HVR-1 Region

FIGURE 5: Agarose gel electrophoresis of first six amplifications of mtDNA.

Sample # SNPs (C16223T indicates substitution of C at position 16223 in reference sequence with T in sample analyzed)

Haplogroup(mtDNA type)

Cancer Status

P14 C16223T A16235G C16278T C16294T A16309G

L2 Triple positive

P22 16111T 16129A 16185G 16223T 16234T 16290T 16319G 16363C

A Triple positive

P24 T16032G A16151C A16154C A16170C A16191T A16249C C16323T C16378T T16411C

H Triple positive

RESULTS

HVR-1 sequence was confirmed for three samples, and single nucleotide polymorphisms (SNPs) were identified using Chromas Lite. The identified SNPs were used to determine the mtDNA type (haplogroup) using The Genographic Project, Haplogroup Prediction Tool.

The amplified and sequenced HVR-1 region of each sample was compared to the Cambridge Reference Sequence (CRS), the first mitochondrial DNA sequence published in 1987 and belonging to haplogroup H. This is a mtDNA type prevalent in European populations.

FUTURE DIRECTIONS AND IMPACT OF WORK

REFERENCESCarey LA, Perou CM, Livasy CA, Dressler LG, Cowan D, Conway K, Karaca G, Troester MA, Tse CK,Edmiston S, Deming SL, Geradts J, Cheang MC, Nielsen TO, Moorman PG, Earp HS, Millikan RC.Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA. 2006 Jun7;295(21):2492-502.

Stark A, Kleer CG, Martin I, Awuah B, Nsiah-Asare A, Takyi V, Braman M, Quayson SE, Zarbo R,Wicha M, Newman L. African ancestry and higher prevalence of triple-negative breast cancer:findings from an international study. Cancer. 2010 Nov 1;116(21):4926-32.

http://4.bp.blogspot.com

/_K7q0QX9ib3s/TSXNAMF-xUI/

AAAAAAAAD6U/EnptP8gh2x4/s1600/mixed.jpg

http://64.40.115.138/file/lu/6/52235/

NTIyMzV9K3szNDIwOTI=.jpg?download=1