<p>Supplementary Table S1. The outlier mRNA expression profiles of the gene tissue index (GTI) outlier analysis. The list of 2415 outlier genes in GIST is ranked by the gene tissue index.</p>
Background. Adaptation to local habitat conditions may lead to the natural divergence of populations in life-history traits such as body size, time of reproduction, mate signaling or dispersal capacity. Given enough time and strong enough selection pressures, populations may experience local genetic differentiation. The genetic basis of many life-history traits, and their evolution according to different environmental conditions remain however poorly understood. Methods. We conducted an association study on the Glanville fritillary butterfly, using material from five populations along a latitudinal gradient within the Baltic Sea region, which show different degrees of habitat fragmentation. We investigated variation in ten principal components, cofounding in total 21 life-history traits, according to two environmental types, and 33 genetic SNP markers from 15 candidate genes. Results. We found that nine SNPs from five genes showed strong trend for trait associations ( p -values under 0.001 before correction). These associations, yet non-significant after multiple test corrections, with a total number of 1086 tests, were consistent across the study populations. Additionally, these nine genes also showed an allele frequency difference between the populations from the northern fragmented versus the southern continuous landscape. Discussion. Our study provides further support for previously described trait associations within the Glanville fritillary butterfly species across different spatial scales. Although our results alone are inconclusive, they are concordant with previous studies that identified these associations to be related to climatic changes or habitat fragmentation within the Åland population.
Abstract Tumor cells leak their DNA into the blood stream, which allows us to use plasma sample from a patient to measure biomarker levels. In particular, circulating tumor DNA (ctDNA) sampling together with next-generation sequencing technologies provide a rapid and noninvasive test for quantifying tumor response to a treatment as well as finding potentially actionable mutations. The main objective of our study was to use ctDNA to establish a therapeutic window for targeting potentially actionable mutations to optimize the treatment of high-grade serous ovarian cancer (HGSOC) patients. We employed a targeted sequencing panel of 508 clinically annotated cancer genes to screen for actionable copy-number variations (CNV) and single-nucleotide variants (SNV) in 56 plasma and 20 fresh tumor samples from 13 patients with stage IIB-IVB HGSOC treated at the Turku University Hospital, Finland. All patients were surgically debulked and had received standard first-line carboplatin and paclitaxel chemotherapy. We analyzed longitudinal samples (from 3-6 time points per patient) from 11 patients during primary therapy, and from two patients with multiple (two and three samples per patient) relapsed disease. DNA isolated from tumor tissue and plasma was analyzed for genetic alterations by targeted deep-sequencing. White blood cell DNA was used as germline controls. Pathogenic germline mutations in 14 known ovarian cancer susceptibility genes were evaluated with CADD annotation framework and ClinVar database. Minimum requirements for passed somatic SNVs were CADD phred score 10, sequencing depth 100 (ctDNA) or 30 reads (tumor and blood), variant read count 4 or frequency 0.001. Variants detected in blood with > 2 reads were excluded. Additionally, a variant that passed filtering in at least one sample of a patient was included, regardless of threshold, if present in any other specimen. Thresholds of < 0.7 and > 4 copies were used as functionally relevant losses and gains, respectively. Clinically relevant germline pathogenic mutations in BRCA2, ATR, APC, and RB1 genes were identified from blood samples of five (38%) patients. The preoperative samples were also characterized by the highest somatic mutation burden, with a median total variant allele frequency (VAF) of 0.16 (range 0.02-0.77). Importantly, clinically relevant CNVs were detected in preoperative ctDNA of 6 (46%) patients, in potentially targetable driver genes such as ERBB2, PIK3CA, and CDK12. In six patients undergoing neoadjuvant chemotherapy (NACT), we noted a significant decrease in total ctDNA mutation burden during treatment, consistent with a drop in CA-125 levels. Interestingly, the levels of CNV counts increased in ctDNA during NACT in two patients, which associated with improved response to chemotherapy. During adjuvant treatment after debulking surgery, potentially actionable mutations were detected in all patients, with median total VAF of 0.03 (range 0.006-0.43). Importantly, in patients with no macroscopic residual disease, we detected a median of 2.5 (range 1-21) mutations in adjuvant treatment samples, indicating a molecularly persistent disease. Further, a subset of these alterations in, e.g., FANCA and PRCKB persisted during adjuvant treatment, revealing a potential therapeutic window for targeted treatments. Finally, two patients with progressive disease were characterized by predominantly either ctDNA gains or losses. Further, potentially actionable mutations in, e.g., TNXRD1, which sensitizes to AKT inhibitors, could be identified and tracked during disease progression. Taken together, longitudinal analysis of a panel-based ctDNA targeted sequencing can reliably detect very low VAF alterations, which can be used to identify and track actionable genomic alterations. Thus, ctDNA analysis can open a therapeutic window to target molecular residual disease in patients with newly diagnosed and advanced HGSOC. This abstract is also being presented as Poster B06. Citation Format: Kaiyang Zhang, Liina Salminen, Jaana Oikkonen, Kaisa Huhtinen, Johanna Hynninen, Seija Grénman, Sakari Hietanen, Rainer Lehtonen, Anniina Färkkilä, Sampsa Hautaniemi. Longitudinal sampling of ctDNA reveals actionable mutations to optimize treatment of patients with high-grade serous ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr PR08.
Abstract A key event in cancer progression is the establishment of an immunosuppressive environment that prevents the immune system from effectively attacking the cancer cells. In this study we aim to characterize the cellular determinants and the spatial features of immune suppressive mechanisms in high-grade serous ovarian cancer (HGSOC) via integrating tissue Cyclic Immunofluorescence (tCycIF), a novel highly multiplexed single-cell spatial proteomics platform with multi-omics data, including state-of-the-art single-cell RNA sequencing. We have conducted a comprehensive analysis of a unique dataset consisting of 23 HGSOC samples, including 7 pairs of treatment-naïve and post-chemotherapy samples, using tCycIF, single-cell, and bulk RNA sequencing coupled with novel deconvolution algorithms and whole-genome sequencing. All samples were prospectively collected from patients treated at Turku University Hospital, Finland, as a part of the HERCULES consortium. Our preliminary findings suggest that tCycIF can reliably capture tumor microenvironment composition in HGSOC. Overall, there was a good correlation with tumor purity between all the methods used. In tCycIF, scRNAseq and bulk deconvolution macrophages were the most common immune cell type in the HGSOC microenvironment. However, specific immune subpopulations, such as CD8+T-cells, had a larger proportion in tCycIF compared to single-cell RNA sequencing and bulk-deconvoluted RNAseq data. Further, the immune profiling based on RNAseq deconvolution algorithm showed highly variable results based on the algorithm used. We are in the process of using our complete dataset to compare state-of-the-art methods and improve algorithms for HGSOC immunophenotyping. tCycIF’s spatial proteomic data in single-cell resolution allows us to gain new insights into the tumor microenvironment and discover the previously latent cell-to-cell interactions that make up the immunosuppressive milieus in HGSOC tumors. The improvement of novel reliable single-cell immunophenotyping methods is critical to develop more effective immunotherapies to improve the outcomes and survival of patients with HGSOC. Citation Format: Miikka K. Kilkkila, Julia Casado, Connor Jacobson, Antti Hakkinen, Erdogan Erkai, Jun Dai, Kaiyang Zhan, Zoltan Maliga, Olli Carpen, Rainer Lehtonen, Sampsa Hautaniemi, Peter Sorger, Anna Vaharautio, Anniina Farkkila. Integrating highly-multiplexed imaging with multi-omics data to uncover immunologic vulnerabilities in high-grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B62.
Background Molecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Åland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001. Principal Findings A cDNA library of a pooled sample of fungal conidia was sequenced on the 454 GS-FLX platform. Over 549,411 reads were obtained and annotated into 45,245 contigs. Annotation data was acquired for 65.2% of the assembled sequences. The transcriptome assembly was screened for SNP loci, as well as for functionally important genes (mating-type genes and potential effector proteins). A genotyping assay of 27 SNP loci was designed and tested on 380 infected leaf samples from 80 populations within the Åland archipelago. With this panel we identified 85 multilocus genotypes (MLG) with uneven frequencies across the pathogen metapopulation. Approximately half of the sampled populations contain polymorphism. Our genotyping protocol revealed mixed-genotype infection within a single host leaf to be common. Mixed infection has been proposed as one of the main drivers of pathogen evolution, and hence may be an important process in this pathosystem. Significance The developed SNP panel offers exciting research perspectives for future studies in this well-characterized pathosystem. Also, the transcriptome provides an invaluable novel genomic resource for powdery mildews, which cause significant yield losses on commercially important crops annually. Furthermore, the features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and hence our results provide methodological insights from SNP calling to field sampling protocols for a wide range of biological systems.
Abstract Background Ephrin receptor B2 ( EPHB2 ) has recently been proposed as a novel tumor suppressor gene in colorectal cancer (CRC). Inactivation of the gene has been shown to correlate with progression of colorectal tumorigenesis, and somatic mutations have been reported in both colorectal and prostate tumors. Methods Here we have analyzed the EPHB2 gene for germline alterations in 101 individuals either with 1) CRC and a personal or family history of prostate cancer (PC), or 2) intestinal hyperplastic polyposis (HPP), a condition associated with malignant degeneration such as serrated adenoma and CRC. Results Four previously unknown missense alterations were observed, which may be associated with the disease phenotype. Two of the changes, I361V and R568W, were identified in Finnish CRC patients, but not in over 300 Finnish familial CRC or PC patients or more than 200 population-matched healthy controls. The third change, D861N, was observed in a UK HPP patient, but not in additional 40 UK HPP patients or in 200 UK healthy controls. The fourth change R80H, originally identified in a Finnish CRC patient, was also found in 1/106 familial CRC patients and in 9/281 healthy controls and is likely to be a neutral polymorphism. Conclusion We detected novel germline EPHB2 alterations in patients with colorectal tumors. The results suggest a limited role for these EPHB2 variants in colon tumor predisposition. Further studies including functional analyses are needed to confirm this.
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