The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry

<div><p>The Bene Israel Jewish community from West India is a unique population whose history before the 18^th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on F_ST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.</p></div

ADMIXTURE analysis for Jewish, Indian, Pakistani, Middle Eastern (Druze, Bedouin and Palestinians) and representative HapMap (CEU, YRI, JPT and CHB) populations.

<p>K, the number of clusters, varies from K = 3 to K = 8. We colored some of the populations names based on the following groups: Bene Israel (purple), Jews (red), Indian (blue) and Middle-Eastern (green). See also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152056#pone.0152056.s003" target="_blank">S3 Fig</a>.</p

Founder events in Bene Israel population.

<p>(A) Total lengths of runs of homozygosity (ROH) in Jewish, Indian and HapMap populations. The larger variance in ROH values in some Indian populations is due to smaller sample size. (B-C) Autocorrelation in Bene Israel pairs, as a function of the genetic distance, after subtracting the autocorrelation between Bene Israel and other (B) Jewish and (C) Indian populations. Blue and red lines correspond to the fitted curve based on a single and two founder events, respectively.</p

Principal Component Analysis of Jewish, Indian and worldwide populations.

<p>Each panel presents the top two principal components for a set of populations that include Bene Israel together with: (A) Jewish, Indian, Pakistani, Middle Eastern and four worldwide HapMap populations (CEU, CHB, JPT and YRI); (B) Jewish, Middle-Eastern, Pakistani and Indian populations; (C) Indian and Pakistani populations; (D) Jewish, Middle-Eastern and Pakistani populations. Abbreviations of Jewish populations: Bene Israel (Bene), Algerian Jews (ALGJ), Ashkenazi Jews (ASHJ), Djerban Jews (DJEJ), Georgian Jews (GEOJ), Greek Jews (GRKJ), Iranian Jews (IRNJ), Iraqi Jews (IRQJ), Italian Jews (ITAJ), Libyan Jews (LIBJ), Moroccan Jews (MORJ), Syrian Jews (SYRJ), Tunisian Jews (TUNJ), Yemenite Jews (YMNJ).</p

Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer.

Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio ((w)HR) = 1.09 (95% CI 1.02-1.16), p(trend) = 0.017; and n = 3,965, (w)HR = 1.04 (95% CI 0.94-1.16), p(trend) = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM

Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast

Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio (wHR) = 1.09 (95% CI 1.02–1.16), ptrend = 0.017; and n = 3,965, wHR = 1.04 (95% CI 0.94–1.16), ptrend = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM.This work was funded by the Spanish Ministries of Health, and Science ane Innovation (CB07/02/2005; FIS 08/1120, 08/1359, 08/1635, and 09/02483; RTICCC RD06/0020/1060 and RD06/0020/0028; Transversal Action Against Cancer; the Spanish Biomedical Research Centre Networks for Epidemiology and Public Health, and Rare Diseases; and the ‘‘Ramón y Cajal’’ Young Investigator Program), the Spanish National Society of Medical Oncology (2010), the SpanishAssociation Against Cancer (AECC 2010), the AGAUR Catalan Government Agency (2009SGR1489 and 2009SGR293; and the Beatriu Pinós Postdoctoral Program), the Ramón Areces Foundation (XV), the ‘‘Roses Contra el Caàncer’’ Foundation, the Michael Cuccione Foundation for Childhood Cancer Research, Cancer Research–UK (C490/A10119, C1287/A8874, C1287/A10118, C5047/A8385, and C8197/A10123), the National Institute for Health Research (UK), the Association for International Cancer Research (AICR-07-0454), the Ligue National Contre le Cancer (France), the Association ‘‘Le cancer du sein, parlons en!’’, the Dutch Cancer Society (NKI 1998–1854, 2004–3088, and 2007–3756), the Fondazione Italiana per la Ricerca sul Cancro (‘‘Hereditary Tumors’’), the Associazione Italiana per la Ricerca sul Cancro (4017), the Italian Ministero della Salute (RFPS-2006-3-340203 and ‘‘Progetto Tumori Femminili’’), the Italian Ministero dell’Universita’ e Ricerca(RBLAO3-BETH), the Fondazione IRCCS Istituto Nazionale Tumori (INT ‘‘561000’’), the Fondazione Cassa di Risparmio di Pisa (Istituto Toscano Tumori), the National Breast Cancer Foundation (Australia), the Australian National Health and Medical Research Council (145684, 288704, and 454508), the Queensland Cancer Fund, the Cancer Councils of New South Wales, Victoria, Tasmania, and South Australia, the Cancer Foundation of Western Australia, the German Cancer Aid (107054), the Center for Molecular Medicine Cologne (TV93), the National Cancer Institute (USA; CA128978 and CA122340), National Institutes of Health (RFA-CA-06-503, BCFR U01 CA69398, CA69417, CA69446, CA69467, CA69631, and CA69638), the Research Triangle Institute Informatics Support Center (RFP N02PC45022-4/n6), the Specialized Program of Research Excellence (SPORE P50 CA83638 and CA113916), the Department of Defense Breast Cancer Research Program (05/0612), the Eileen Stein Jacoby Fund, the Breast Cancer Research Foundation, the Marianne and Robert MacDonald Foundation, the Komen Foundation, the Helsinki University Central Hospital Research Fund, the Academy of Finland (110663), the Finnish Cancer Society, the Sigrid Juselius Foundation, and the EU FP7 (223175,HEALTH-F2-2009-223175). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip