Association of cell-free DNA (cfDNA) levels with myeloid-derived suppressor cells (MDSC) levels in blood of patients (pts) with muscle invasive (MI) and metastatic (met) bladder cancer (BC)

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Background: cfDNA can be detected in healthy individuals but higher concentrations are present in pts with cancer. MDSC are immature immunosuppressive cells that can be mobilized from bone marrow by tumor-related factors. Higher blood MDSC levels have been associated with worse outcomes in pts with solid tumors including BC. We assessed correlations between cfDNA and MDSC levels in pts with MIBC and met BC. Methods: Peripheral blood from pts with MIBC and met BC was collected in Streck BCT tubes and processed to obtain cf nucleic acid extracts. Total cfDNA was determined by fluorimetry. Cell-free DNA fragment size was measured by Bioanalyzer DNA analysis; 100-400 bp fragments (mono- and di-nucleosomal fragments linked to granulocytic processing of apoptotic and necrotic tumor cells) were designated low molecular weight (LMW-frags). The % of MDSC (CD33+/HLADR-) and subtypes were measured. MDSC subtypes were defined as polymorphonuclear (PMN-MDSC: CD15+/CD14-), monocytic (M-MDSC: CD15-/CD14+) and uncommitted (UNC-MDSC: CD15-/CD14-). Spearman’s correlation test was used for analysis. Results: Blood from 37 pts (19% women, 40% never smokers) with MIBC or met BC was collected: 15 (41%) with MIBC and 22 (59%) with met BC at time of collection. There was a significantly positive correlation between total MDSC and cfDNA levels (r = 0.57, P = 0.0003). Among MDSC subtypes, there was a significantly positive correlation between PMN-MDSC and cfDNA levels (r = 0.61, P < 0.0001). The higher level of LMW-frags was significantly but moderately associated with higher total MDSC (r = 0.43, P 0.008) and PMN-MDSC (r = 0.41, P 0.01) levels. There was no significant correlation between cfDNA level and other MDSC subtypes. Conclusions: There was a positive correlation between total and PMN-MDSC with cfDNA levels in blood from pts with MIBC and met BC. That may suggest a putative role for MDSC in mediating cfDNA release into the circulation, consistent with prior reports of granulocyte-mediated ctDNA processing. Further studies need to identify mechanisms and implications of our findings and potential correlation with clinical outcomes.

Circulating cell-free DNA (cfDNA) levels and fragmentation pattern can distinguish nonmuscle invasive (NMI) from muscle-invasive (MI) and metastatic (met) bladder cancer (BC)

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Background: Occult MI and met BC may be under-staged. Circulating cfDNA may be a dynamic, low-cost and minimally invasive biomarker. We evaluated correlations between total circulating cfDNA and presence of MIBC and met BC. We hypothesized that the relative abundance of circulating low molecular weight cfDNA would correlate with BC stage. Methods: Peripheral blood from pts with BC was collected in Streck BCT tubes and processed to obtain cf nucleic acid extracts. Total cfDNA quantity (ng/ml) was assessed by fluorimetry. cfDNA fragment size was measured by Bioanalyzer DNA analysis. Wilcoxon rank sum test and Fisher’s Exact test were used to compare cfDNA quantity and fragmentation pattern among pts with NMIBC, MIBC, met BC. Results: Blood was obtained from 58 pts with BC (20% women, 34% never smokers, median age 71 (29-89). There was no significant difference in cfDNA between MIBC and met BC, however, it was significantly lower in pts with NMIBC vs MIBC and met BC (table). The concentration of low molecular weight fragments (LMW-frags) (100 - 400) base pairs and the ratio of LMW-Frag to cfDNA were significantly different between pts with NMIBC and pts with MIBC or met BC (table). Using median values as the cutoff, there was a significantly higher proportion of pts with cfDNA > 7 ng/ml and LMW-frags > 1.6 ng/mL, in MIBC & met BC vs NMIBC (p < 0.001). The % of pts with LMW-frags to cfDNA > 30%, was significantly different among NMIBC, MIBC and met BC groups: 16%, 53%, 78%, respectively (p < 0.001). Conclusions: This exploratory study suggests that cfDNA levels may correlate with BC stage. Measuring the relative abundance of LMW-frags with the expected size of cf DNA can enhance the specificity of cfDNA analysis for distinction between MIBC and met BC. Further studies are needed to confirm findings and define the optimal cut-points for optimal BC staging. [Table: see text]

Identification of gene expression determinants of radiosensitivity in bladder cancer (BCa) cell lines

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Background: Trimodality therapy with TURBT followed by concurrent chemoradiation is an alternative to cystectomy in selected patients with muscle invasive BCa. Identifying genetic determinants of radiation response may help select patient for organ-sparing treatments with curative intent. Methods: Molecular characterization of 20 cell lines was previously performed, including mutation analysis, CNA (high density SNP arrays) and gene expression (RNAseq). Cell line identity was authenticated by genomic fingerprinting. We performed colony forming assays (CFA) and cumulative survival was quantified using the area under the cell survival curve (AUC, range 0-8Gy) to create a radiosensitivity index. Pre and post-radiation proliferative capacity was determined by cell titer glo (CTG) assay. Gene (R v3.5.1) and network (Ingenuity Pathyway Analysis) level expression differences were determined as a function of AUC to identify biologically relevant associations with radiation response. Results: Of 20 cell lines (7 basal, 13 luminal subtype), both CFA and CTG data was successfully obtained for 13 cell lines (6 basal, 7 luminal) treated with high dose rate (HDR) radiation. AUCs for the colony forming assay (CFA) survival curves ranged 1.79-3.27. RNAseq identified 18,634 unique transcripts mapping to distinct loci and 196 genes were identified with AUC correlation p values <0.01 (FDR <0.5, mean FPKM>0.5). These genes were strongly enriched for membership in the peroxisome proliferator (PPAR) pathway (IPA, p = 9.40E-03) and STAT3 pathway (IPA, p = 1.56E-3). Validation studies confirmed PPARγ, ICAM2, JAK3, IL1B, OAS1 and OAS2 genes to be associated with differential response to radiation, with expression upregulated in radio-resistant cells. A basal subtype was strongly associated with a radiosensitive phenotype (Chi-Squared χ2 p=0.0083). Conclusions: BCa radio-sensitivity was associated with baseline gene expression differences in vitro. The basal subtype and repression of either the PPAR or STAT3 pathways predicted increased radiosensitivity. This study nominates candidate biomarkers for mechanistic studies and clinical validation in BCa.

A linguistically informed autosomal STR survey of human populations residing in the greater Himalayan region

The greater Himalayan region demarcates two of the most prominent linguistic phyla in Asia: Tibeto-Burman and Indo-European. Previous genetic surveys, mainly using Y-chromosome polymorphisms and/or mitochondrial DNA polymorphisms suggested a substantially reduced geneflow between populations belonging to these two phyla. These studies, however, have mainly focussed on populations residing far to the north and/or south of this mountain range, and have not been able to study geneflow patterns within the greater Himalayan region itself. We now report a detailed, linguistically informed, genetic survey of Tibeto-Burman and Indo-European speakers from the Himalayan countries Nepal and Bhutan based on autosomal microsatellite markers and compare these populations with surrounding regions. The genetic differentiation between populations within the Himalayas seems to be much higher than between populations in the neighbouring countries. We also observe a remarkable genetic differentiation between the Tibeto-Burman speaking populations on the one hand and Indo-European speaking populations on the other, suggesting that language and geography have played an equally large role in defining the genetic composition of present-day populations within the Himalayas.

Genetic structure of Indian populations based on fifteen autosomal microsatellite loci

Background

Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers.

Results

The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively.

Conclusion

Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.

Deletions in the Y-derived amelogenin gene fragment in the Indian population

Background

Rare failures in amelogenin-based gender typing of individuals have been observed globally. In this study, we report the deletion of a large fragment of the amelogenin gene in 10 individuals out of 4,257 male samples analyzed from 104 different endogamous populations of India.

Methods

Samples were analyzed using commercial genetic profiling kits. Those that exhibited failures in amelogenin-based gender identification were further analyzed with published as well as newly designed primers to ascertain the nature and extent of mutation.

Results

The failure rate among Indian males was 0.23 %. Though the exact size and nature of the deletion (single point mutations at a number of positions or a single large deletion) could not be determined in the present study, it is inferred that the deletion spans a region downstream of the reverse primer-binding site of commercially available amelogenin primer sets. Deletions were conspicuously absent among the Mongoloid tribes of Northeast India, while both caste and tribal groups harbored these mutations, which was predominantly among the Y-chromosomes belonging to J2 lineage.

Conclusion

Our study indicates that the different amelogenin primer sets currently included in genetic profiling multiplex kits may result in erroneous interpretations due to mutations undetectable during routine testing. Further there are indications that these mutations could possibly be lineage-specific, inherited deletions.

Molecular insights into the origins of the Shompen, a declining population of the Nicobar archipelago

The Shompen, one of the most isolated and poorly understood contemporary hunter-gatherer populations, inhabit Great Nicobar Island, the southernmost island of the Nicobar archipelago. Morphological imprints in the Shompen were interpreted to favour a mixed Indo-Chinese, Malay, Negrito and Dravidian origin. Analyses of the mitochondrial, Y-chromosomal and autosomal gene pool of contemporary Shompen have revealed low diversity, illustrating a founder effect in the island population. Mitochondrial sequence analyses revealed the presence of two haplogroups of R lineage: B5a, and a newly defined clade, R12. Y-chromosomal analyses demonstrated the occurrence of a single lineage found predominantly in Austro-Asiatic speakers across Asia. With the different types of genetic markers analysed, the Shompen exhibit varying levels of genetic relatedness with the Nicobarese, and Austro-Asiatic speakers of mainland India and Southeast Asia. These genetic analyses provide evidence that the Shompen, an offshoot of the Nicobarese, are descendants of Mesolithic hunter-gatherers of Southeast Asian origin, deriving from at least two source populations.

A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios

Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.

Microsatellite Diversity among Three Endogamous Tamil Populations Suggests Their Origin from a Separate Dravidian Genetic Pool

The genetic profiles based on 15 autosomal microsatellite markers were analyzed among three socially distinct endogamous Dravidian populations: Tanjore Kallar, Vanniyar, and Pallar of Tamil Nadu, southern India, in order to understand their origin and the extent of genetic affinity and diversity among them. All loci were highly polymorphic and followed Hardy-Weinberg expectations except for loci D13S317 in Tanjore Kallars and D7S820 in Vanniyars. The SK2 criterion test showed no evidence of association among the 15 loci in the studied populations. The extent of gene differentiation among the three populations was low (G(ST) = 0.012), suggesting proximity between them. The phylogenetic dendrogram based on allele frequencies places them in a separate cluster, away from other compared Indo-European populations. The fit of the Harpending and Ward model of regression was found to be good and consistent with the extent of endogamy followed by the respective populations. These findings support a separate origin of the Dravidians and reveal an overall genetic unity among the studied Tamil populations belonging to different strata of the social hierarchy. The extent of diversity found among them probably resulted from the strict endogamous practices that they follow.