抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Cardiomyocytes derived from human embryonic stem (hES) cells potentially offer large numbers of cells to facilitate repair of the infarcted heart. However, this approach has been limited by inefficient differentiation of hES cells into cardiomyocytes, insufficient purity of cardiomyocyte preparations and poor survival of hES cell-derived myocytes after transplantation. Seeking to overcome these challenges, we generated highly purified human cardiomyocytes using a readily scalable system for directed differentiation that relies on activin A and BMP4. We then identified a cocktail of pro-survival factors that limits cardiomyocyte death after transplantation. These techniques enabled consistent formation of myocardial grafts in the infarcted rat heart. The engrafted human myocardium attenuated ventricular dilation and preserved regional and global contractile function after myocardial infarction compared with controls receiving noncardiac hES cell derivatives or vehicle. The ability of hES cell-derived cardiomyocytes to partially remuscularize myocardial infarcts and attenuate heart failure encourages their study under conditions that closely match human disease.

https://courses.washington.edu/conj504/readings/murry_reading2.pdf

Cardiomyocytes derived from human embryonic stem cells in pro-survival factors enhance function of infarcted rat hearts

Metastasis, the dissemination and growth of neoplastic cells in an organ distinct from that in which they originated, is the most common cause of death in cancer patients. This is particularly true for pancreatic cancers, where most patients are diagnosed with metastatic disease and few show a sustained response to chemotherapy or radiation therapy. Whether the dismal prognosis of patients with pancreatic cancer compared to patients with other types of cancer is a result of late diagnosis or early dissemination of disease to distant organs is not known. Here we rely on data generated by sequencing the genomes of seven pancreatic cancer metastases to evaluate the clonal relationships among primary and metastatic cancers. We find that clonal populations that give rise to distant metastases are represented within the primary carcinoma, but these clones are genetically evolved from the original parental, non-metastatic clone. Thus, genetic heterogeneity of metastases reflects that within the primary carcinoma. A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell. At least five more years are required for the acquisition of metastatic ability and patients die an average of two years thereafter. These data provide novel insights into the genetic features underlying pancreatic cancer progression and define a broad time window of opportunity for early detection to prevent deaths from metastatic disease.

SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

/pdf/landscape-of-somatic-mutations-in-560-breast-cancer-whole-2ybzc9y4kj.pdf

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double IHC staining. Copy-number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, an FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated patients with PDAC. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected. Implications: Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.

https://aacrjournals.org/mcr/article-pdf/20/5/749/3117598/749.pdf

Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer

Optothermal spectrometry measures the thermal energy produced as a result of absorption by molecules at a given modulation frequency and wavelength. Depending on the modulation frequency used, analysis can be performed in very thin layers (50-150 micrometers). A major advantage of optothermal spectrometry is that it is not very sensitive to light scattering. Haemoglobin in whole blood was measured without any reagent at 16 Hz and 2 Hz frequencies. The precisions (within-series, within-day and between-day) were acceptable, and comparisons with reference methods were excellent. As opposed to the reference methods, optothermal spectrometric determinations were not affected by lipaemia. When measured continuously, the signal for haemoglobin increased due to the packing of erythrocytes towards the light source. By converting soluble fibrinogen into insoluble fibrin, the erythrocyte packing could either be inhibited or stopped, and this process could be monitored by assessing the change in the rate of signal increase for haemoglobin. This principle was utilized to analyse the prothrombin complex; the method was found to have acceptable precision and to be comparable to a routine method.

/pdf/determination-of-haemoglobin-and-prothrombin-complex-in-38mc2cs9kl.pdf

Determination of haemoglobin and prothrombin complex in whole blood using optothermal spectrometry.

High-resolution spectroscopic techniques for studying rare-earth ions in nanoparticles

Nanoscale systems offer key capabilities for quantum technologies that include single qubit control and readout, multiple qubit gate operation, extremely sensitive and localized sensing and imaging, as well as the ability to build hybrid quantum systems. To fully exploit these functionalities, multiple degrees of freedom are highly desirable: in this respect, nanoscale systems that coherently couple to light and possess spins, allow for storage of photonic qubits or light-matter entanglement together with processing capabilities. In addition, all-optical control of spins can be possible for faster gate operations and higher spatial selectivity compared to direct RF excitation. Such systems are therefore of high interest for quantum communications and processing. However, an outstanding challenge is to preserve properties, and especially optical and spin coherence lifetimes, at the nanoscale. Indeed, interactions with surfaces related perturbations strongly increase as sizes decrease, although the smallest objects present the highest flexibility for integration with other systems. Here, we demonstrate optically controlled nuclear spins with long coherence lifetimes (T2) in rare earth doped nanoparticles. We observed spins echoes and measured T2 of 2.9 +/- 0.3 ms at 5 K and under a magnetic field of 9 mT, a value comparable to those obtained in bulk single crystals. Moreover, we achieve, for the first time, spin T2 extension using all-optical spin dynamical decoupling and observe high fidelity between excitation and echo phases. Rare-earth doped nanoparticles are thus the only reported nano-materials in which optically controlled spins with millisecond coherence lifetimes have been observed. These results open the way to providing quantum light-atom-spin interfaces with long storage time within hybrid architectures.

/pdf/all-optical-control-of-long-lived-nuclear-spins-in-rare-1wda28u4yo.pdf

All-optical control of long-lived nuclear spins in rare-earth doped nanoparticles


 Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and was listed as the third cause of death by cancer in 2020 (WHO). Hepatocarcinogenesis is a multistep process and to date it is still poorly understood. HCC occurs almost entirely in patients with underlying chronic liver disease and cirrhosis. Pre-clinical animal models play an important role in unveiling cancer biology which can facilitate development and testing of new antineoplastic drugs. The aim of this study was to establish an orthotopic model of HCC utilizing two cell lines Huh-7 and HepG2, which could be effectively used to study efficacy of new potential treatments. In a follow up study, the correlation of tumor marker alpha-fetoprotein (AFP) and tumor growth was investigated. AFP was measured using Quantikine® ELISA kit. For the intrahepatic (ih) inoculation cancer cells were injected into the left lobe of the liver. For the intrasplenic (is) inoculations of HCC cells, the spleen was exposed, and cells were injected into spleen parenchyma along the long axis of the spleen. Afterwards spleen was removed to avoid intrasplenic tumor growth. The animals were weighed two times a week throughout the study and appearance of any clinical signs was closely monitored. The animals were terminated 70 days after cancer cell implantation. The mice did not present with any acute symptoms before the end stage disease. However, prior sacrifice some swelling and darkening of the abdominal area especially in the ih-model was observed. To visualize liver ExiTron Nano 6000 nanoparticle contrast agent was used. The contrast agent was administered intravenously once during the study, prior the first imaging. Disease progression was monitored using Bruker SkyScan 1276 High-Resolution Micro-CT Scanner. The in vivo measurements were performed using one field of view (FOV) and an image pixel size of 18 μm. Each in vivo scanning was completed within 12 minutes and the estimated radiation dose was kept under 500 mGy at each imaging session. The first tumours were detected by µCT between 2-3 weeks depending more on the cancer cell implantation route than the cell line used. The take rate in the liver was 85% in the ih-model, and less than 50% in the is-model. The intrahepatic inoculation led to more uniform and measurable tumor nodules observed in majority of operated animals, whereas the intrasplenic tumors were dispersed throughout with multiple nodules. In addition, a tight correlation between tumor volume and amount of alpha-fetoprotein detected from serum samples was found. In conclusion, an orthotopic model using intrahepatic approach of cancer cells implantation was established. Application of µCT enabled following tumor growth and recognition of cancer spread in the abdomen. Altogether this provides a promising tool contributing to the development of novel therapies targeting HCC in vivo.
 Citation Format: Justyna Zdrojewska, Mari Suominen, Shirin Katoozi, Katja Fagerlund, Jukka Rissanen, Roger Malerbakken-Bjerke, Jenny Karlsson. Orthotopic model of hepatocellular carcinoma (HCC) using Huh-7 and HepG2: Application of micro-CT in detection of cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1662.

Jenny Karlsson

Papers

Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer

Determination of haemoglobin and prothrombin complex in whole blood using optothermal spectrometry.

High-resolution spectroscopic techniques for studying rare-earth ions in nanoparticles

All-optical control of long-lived nuclear spins in rare-earth doped nanoparticles

Abstract 1662: Orthotopic model of hepatocellular carcinoma (HCC) using Huh-7 and HepG2: Application of micro-CT in detection of cancer progression