Fraction Of Clones Research Articles

Abstract 3793: Single-cell transcriptional lineage tracing reveals complexity and plasticity of breast cancer pro-metastatic phenotypes

Abstract Breast cancer (BC) represents a major clinical hurdle, with metastasis being the most devastating events in patients’ history. Traditional lineage tracing approaches have been widely employed to study the metastatic progression of BC. However, these approaches were limited to the investigation of clonal dynamics and did not provide detailed molecular information underlying the pro-metastatic phenotype. In this work, we exploited a library of degenerated barcodes which were both integrated in the genome and expressed as synthetic transcripts. Coupling this barcoding strategy to scRNA-seq analysis, we tracked the clonal and transcriptional evolution of more than 37,000 MDA-MB-231 (a human triple-negative BC cell line) cells in vivo. Clonal distribution analysis revealed that BC clones display proliferative heterogeneity in primary tumors, with a small fraction of clones outcompeting all the others. Furthermore, primary breast tumors turned out to be composed of two phenotypically distinct groups of clones: highly proliferative, on one side, and migratory/stressed/stem-like, on the other. Then, we showed that the striking majority of metastatic cells derived from a single clone which was under-represented in its primary tumor. Importantly, these pro-metastatic clones upregulated genes and pathways associated with extracellular matrix (ECM) interaction, migration, and type-I interferon (IFN) response. In this scenario, independent pro-metastatic clones heterogeneously upregulated these pathways, thus suggesting a multi-faceted functional phenotype. Despite this variability, we detected a set of genes whose expression was statistically associated with the pro-metastatic phenotype, and we validated the relevance of these molecular features both at the biological and clinical level. First, we observed a reduced metastatic burden upon the in vivo knock-down of genes involved in ECM interaction (e.g., ANGPTL4, KCNQ1OT1, and ITGB4) and type-I IFN response (e.g., LY6E and IFI6). Second, we derived two compact gene signatures showing robust predictive power of BC patient survival, independently of other known clinical factors. In conclusion, our work revealed previously unappreciated cellular mechanisms of BC metastasization, providing new actionable therapeutic targets and new molecular predictors of BC prognosis. Citation Format: Niccolò Roda, Andrea Cossa, Federica Ruscitto, Chiara Priami, Giada Blandano, Alberto Dalmasso, Francesco Bertolini, Pier Giuseppe Pelicci. Single-cell transcriptional lineage tracing reveals complexity and plasticity of breast cancer pro-metastatic phenotypes [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 3793.

Fully Automated Workflows Quantify and Report Key T-Cell and B-Cell Receptor Biomarkers Relevant to Immuno-Oncology and Heme-Oncology Research

BackgroundT-cell and B-cell repertoire analysis is used in oncology research, to understand the etiology of complex disease phenotypes, for the identification of biomarkers predictive of disease burden, outcome, and response to treatment, and for research in diagnosis and recurrence monitoring. Key predictors include secondary and tertiary repertoire features not reported by existing sequencing software solutions. For example, due to ongoing somatic hypermutation in mature B-cell receptors, the underlying sequence of a given clone can accumulate base differences and appear as several distinct clones with smaller frequencies, thereby hampering the ability of analysis software to detect its presence as a single dominant clone with the highest frequency. This has particularly detrimental implications for research in disorders such as follicular lymphoma and may require clonal lineage analysis for proper mitigation. Therefore, to aid the downstream analytics of biomarker identification and the study of complex disease, we developed fully automated analysis solutions that directly compute and report several key features (clonal lineage, amongst several others described below) pertinent to this area of research.ResultsWe developed the Oncomine™ TCR Beta-SR, TCR Gamma-SR, BCR IGH-SR and BCR IGKL-SR workflows on Ion Reporter™ to characterize T-cell (β, γ chains) and B-cell (heavy and light (κ, δ) chains) repertoires. These workflows generate output tables and visualizations for primary repertoire features such as detected clones (viz., unique rearrangements in the receptor DNA sequence), their frequencies, as well as their somatic hypermutation levels in the case of B-cells (Figure 1a & 1b) for clonality assessment and rare clone detection. The software also quantifies and reports several secondary and tertiary repertoire features in a sample, such as clonal diversity, evenness of the clonal population, and B-cell lineage groupings useful in identifying related sub-clones. It includes spectratyping format plots to simultaneously assess the above features as a function of v-gene usage and CDR3 length combinations (Figure 1c & 1d), thereby providing users a complete snapshot of the repertoire, and also the capability to quickly determine CDR3 lengths and V-gene usage of highly expanded or mutated clones. A separate CDR3 lengths histogram is included, as well as a heatmap that depicts the distributions/intensity of Variable-Joining gene combinations (Figure 1e & 1f).Furthermore, the TCR workflows also report (i) convergence frequencies (fraction of clones with different nucleotide sequences, but identical amino acid sequences), and (ii) haplotype grouping for an analyzed sample, based on V-gene allele genotyping and clustering (Figure 1g). In addition, the long read Oncomine™ BCR IGH-LR workflow uniquely reports the isotype class for every detected clone, and includes a visualization of total reads, clones and lineages in the sample represented by isotype (Figure 1h).ConclusionThe Oncomine™ immune repertoire workflows for T-cell and B-cell receptor sequencing were designed to be of high utility in distinct areas of malignancy research, and we expect them to greatly simplify complex downstream analyses. The unique capabilities of the workflows to automatically report secondary and tertiary repertoire features such as (i) clonal lineages for improved dominant clone detection in blood cancers, (ii) TCR clone convergence for prediction of response to immune checkpoint inhibitors [1,2], (iii) TCR haplotype grouping for evaluation of risk factors for autoimmunity and immune-related adverse events [3], and (iv) isotype classification in BCRs for studying pan-cancer immune evasion mechanisms, demonstrate the clear advantages of using these automated workflows over other existing solutions.For research use only.References1) Looney TJ et al. (2020) TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer. Front. Immunol. 10:2985.2) Naidus et al. (2021) Early changes in the circulating T cells are associated with clinical outcomes after PD-L1 blockade by durvalumab in advanced NSCLC patients. Cancer Immunology, Immunotherapy 70:2095-21023) Looney TJ et al. (2019) Haplotype Analysis of the T-Cell Receptor Beta (TCRB) Locus by Long-amplicon TCRB Repertoire Sequencing. Journal of Immunotherapy and Precision Oncology. 2 (4): 137-143. [Display omitted] DisclosuresSarda: Thermo Fisher Scientific: Current Employment. Lowman: Thermo Fisher Scientific: Current Employment. Toro: Thermo Fisher Scientific: Current Employment. Pickle: Thermo Fisher Scientific: Current Employment. Looney: Thermo Fisher Scientific: Ended employment in the past 24 months; Singular Genomics: Current Employment. Hyland: Thermo Fisher Scientific: Current Employment.

Abstract 1202: Genetically inferred telomere length is associated with clonal copy number alterations in peripheral leukocytes

Abstract Telomeres are DNA-protein structures at the ends of chromosomes essential in maintaining chromosomal stability. Telomeres shorten with each cell division due to incomplete replication of the 3' DNA end resulting in age-related telomere attrition. Very short telomeres induce cellular senescence and/or apoptosis, but cancer cells can bypass this mechanism by upregulating telomerase, TP53 and/or RB. Recent observational studies have identified associations between longer telomeres and elevated cancer risk, including hematologic malignancies; but biologic mechanisms relating telomere length to cancer etiology remain unclear. Our study sought to better understand the links between telomere length and cancer risk by evaluating relationships between telomere length and (1) the acquisition of somatic copy number alterations (SCNAs), (2) the chromosomal distribution and copy number state of acquired SCNAs, and (3) the cellular fraction of clones carrying SCNAs. Genomic data were derived from 431,507 participants in the UK Biobank with genotyping array data (Affymetrix UK BiLEVE Axiom and Biobank Axiom arrays). Telomere length was genetically inferred using a polygenic risk score based on effect estimates and allelic counts of 20 common variants associated with leukocyte telomere length and subsequently standardized. SCNAs were called using raw genotyping array intensity data to detect allelic imbalances (BAF) and deviations from expected intensity (log R ratio) along with data on haplotype imbalances as implemented in MoChA. In total, 15,236 (3.5%) of individuals had a detectable clonal SCNA on an autosomal chromosome. Overall, longer genetically inferred telomere length was positively associated with the presence of an autosomal SCNA (OR=1.07, 95% CI=1.05-1.09, P=1.10 × 10−15). We noted no differences in estimates among strata of chromosomal event location (e.g., telomeric ends, interstitial or whole chromosome event; P= 0.34), suggesting no preference in the type of event associated with inferred telomere length. Likewise, event copy number status demonstrated similar effect sizes across strata of copy number state (e.g., gain, loss, neutral, and unknown events; P= 0.05). When investigating the relationship between inferred telomere length and proportion of cells affected by mosaic SCNAs, longer genetically inferred telomere length was associated with a higher cellular fraction of clones carrying SCNAs (β=0.004, 95% CI= 0.002-0.007, P= 5.60 × 10−4). Cumulatively, our population-based examination of inferred telomere length and SCNAs suggests inherited components of telomere length do not preferentially impact SCNA event location or copy number status, but rather are associated with cellular replicative potential possibly by promoting clonal expansion of leukocytes harboring SCNAs. Citation Format: Derek W. Brown, Shu-Hong Lin, Stephen J. Chanock, Sharon A. Savage, Mitchell J. Machiela. Genetically inferred telomere length is associated with clonal copy number alterations in peripheral leukocytes [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1202.

Clones or no clones: genetic structure of riparian Populus euphratica forests in Central Asia

Many riparian (Tugai) forests growing along rivers in arid and hyper-arid regions of Central Asia are dominated by the Euphrates poplar (Populus euphratica). Besides generative reproduction, which is only possible upon flooding events and at a distance to the groundwater of less than 2 m, this phreatophytic tree species also reproduces vegetatively by forming clones that can cover land surface areas of several hectares. Along a gradient of groundwater distances, we investigated whether the fraction of clones in P. euphratica stands (1) increases with increasing distance to the water table; (2) is higher if supplied with water via river cut-offs; and (3) approaches 100% at a short distance to the groundwater, but at high salt concentrations in the upper soil layers, which would prevent germination and establishment of seedlings. AFLP (Amplified Fragment Length Polymorphism) analyses were conducted on leaf samples taken from mature P. euphratica trees growing at the fringes of the Taklimakan Desert in stands with different distances (2–12 m) to the groundwater at two plots at the middle and the lower reaches of the Tarim River and in a stand close to Ebinur Lake, Xinjiang, China. Genetic diversity was large among plots, but considerably smaller within plots. We found the highest genetic diversity (caused by regeneration from seeds) at plots that have a short distance to the groundwater or are supplied with additional water. There was no significant relationship between groundwater distance and clonal fraction. All investigated trees at the saline Ebinur Lake site belonged to one single clone. Our results demonstrate that the genetic pattern of this widespread species is not easily predictable even over small distances as it is a result of a complex interplay of stand history and dispersal of propagules (pollen, seeds, and vegetative diaspores) by wind and water. In conservation and restoration schemes, P. euphratica stands with a high genetic diversity and stands that grow at short distances to the water table and are regularly subjected to flooding (which favors generative over clonal reproduction) should be prioritized.

Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity

ObjectiveTo identify potential autoreactive B-cell and plasma-cell clones by quantitatively analysing the complete human B-cell receptor (BCR) repertoire in synovium and peripheral blood in early and established rheumatoid arthritis (RA).MethodsThe...

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

MicroRNAs (miRNAs) are processed from primary transcripts that contain partially self-complementary foldbacks. As in animals, the core microprocessor in plants is a Dicer protein, DICER-LIKE1 (DCL1). Processing accuracy and strand selection is greatly enhanced through the RNA binding protein HYPONASTIC LEAVES 1 (HYL1) and the zinc finger protein SERRATE (SE). We have combined a luciferase-based genetic screen with whole-genome sequencing for rapid identification of new regulators of miRNA biogenesis and action. Among the first six mutants analyzed were three alleles of C-TERMINAL DOMAIN PHOSPHATASE-LIKE 1 (CPL1)/FIERY2 (FRY2). In the miRNA processing complex, SE functions as a scaffold to mediate CPL1 interaction with HYL1, which needs to be dephosphorylated for optimal activity. In the absence of CPL1, HYL1 dephosphorylation and hence accurate processing and strand selection from miRNA duplexes are compromised. Our findings thus define a new regulatory step in plant miRNA biogenesis.

Growth dynamics of individual clones of normal human keratinocytes: observations and theoretical considerations

The life histories of 429 individual epidermal keratinocyte clones picked at random were studied. Individual basal keratinocytes were derived from asynchronous rapidly proliferating subconfluent cultures propagated in either a low calcium (0.1mM) or a high calcium (2mM) serum-free medium. Single-celled clones were isolated by seeding trypsin-EDTA dissociated cells into a Petri dish containing cloning chips. Chips with only one cell per chip were transferred into dishes containing either low calcium or high calcium growth factor replete serum-free medium. Clone formation was monitored microscopically and the number of cells in each colony tallied at least twice daily for further analysis. A total of 369 clones were established from seven different neonatal foreskin cell strains (A-F), and 60 clones were derived from one adult human skin cell strain (G). During a five-day culture interval, among 32 clones of strain A, 83% divided at least once, 50% divided once in 24 hours, 86% divided at least three times within three days, and more than 50% divided at least four to five times in five days. Of 231 clones amongst the other five cell strains (B-F), an average of 63% (±12 S,E) divided more than three times in an eight day period, the remainder divided either once, twice or not at all. Of the 106 clones of strain G, reared in high calcium serum-free medium, 67% divided more than three times in a six-day period, and 55% divided five or more times in 6 days. Clones derived from adult skin strain H had a lower clone forming potential with 70% dividing at least once in seven days, and only 30% dividing three or more times. By contrast, the average generation time (AvGT) for second and third passage keratinocytes derived from neonatal foreskin cultures was 24 hrs. Detailed dendrograms were constructed for many of the proliferating clones. The majority of clones expressed a synblastic division pattern with every cell dividing at least once per day. A fraction of clones either exceeded this circadian division rate or displayed a biphasic division pattern with all cells initially dividing once a day and then abruptly slowing to once every other day or to an intermediate rate. A minority of clones was committed to a few terminal divisions. The division patterns of the non-synblastic clones fit an alternating bifurcated branching mode of clonal expansion expressed by the Fibonacci sequence for numbers of accumulated cells per clone per day. These results were analyzed in terms of deterministic, probabilistic and a limit cycle oscillator models of cell division timing.

T cells expressing two different T cell receptors form a heterogeneous population containing autoreactive clones

During T cell development both alleles of the T cell receptor (TCR) alpha locus are rearranged. As a result, a sizeable proportion of T cells can express two distinct TCRs, but the functional significance of this phenomenon remains controversial. Studies on transgenic mice with two TCRs have focused on the risk of immunopathology that such cells may pose, while some have suggested that most dual-specific T cells are nonfunctional or even protective. We tracked the fate and TCR repertoire of single- and dual-specific T cells within a normal polyclonal population undergoing lymphopenia-induced proliferation, a setting which has been shown to cause immunopathology and autoimmunity. After the expansion the repertoire of dual-specific T cells had become highly biased, with both prominent clonal expansions and the complete disappearance of other clones. Our results suggest that the normal repertoire of dual-specific T cells contains both nonfunctional cells and a small, 5% fraction of clones which display a much higher than average affinity to antigens normally tolerated as harmless. This heterogeneity may also help in reconciling some of the earlier, conflicting results.

Characterization of the Aspergillus niger prtT, a unique regulator of extracellular protease encoding genes

Expression of several Aspergillus niger genes encoding major secreted, but not vacuolar, protease genes including the major acid protease gene pepA, was shown to be affected in the previously isolated A. niger protease mutant, AB1.13 [Mattern, I.E., van Noort, J.M., van den Berg, P., Archer, D.A., Roberts, I.N., Hondel, C.A.M.J.J., 1992. Isolation and characterization of mutants of Aspergillus niger deficient in extracellular proteases. Molecular & General Genetics 2, 332–336]. Complementation cloning of the putative protease-regulatory gene affected in this mutant was accomplished using a functional selection approach based on the use of the A. nidulans amdS selection marker driven by the A. niger pepA promoter. As expected the PpepA::amdS selection marker is not expressed in the mutant. Introduction of a self-replicating cosmid library into the mutant strain carrying the PpepA::amdS marker allowed selection of AmdS+ transformants functionally complementing the proposed regulatory mutation. Analysis of complementing cosmid clones revealed that the complementing sequences contained a gene encoding a member of the fungal-specific Zn2Cys6-binuclear cluster protein family. Sequence comparison of the encoded protein, PrtT, showed that it has homologues among different Aspergillus species. The A. oryzae homologue was shown to govern expression of the major alkaline protease AlpA and neutral protease Np1 in this species. In contrast to several other pathway specific regulators, such as AmyR and XlnR, no PrtT orthologues could be found in any other non- Aspergillus (or related) species and surprisingly, also not in Aspergillus nidulans. Interestingly, in all Aspergillus species carrying a prtT orthologue the gene is tightly clustered to a completely syntenous region carrying an amylolytic gene cluster including another Zn2Cys6-binuclear cluster protein, AmyR. Northern analysis of the A. niger prtT gene showed (constitutive) expression from two upstream promoters about 700 bp apart. The presence of several short upstream open reading frames downstream of both the distal and the proximal transcription start point of the prtT gene suggests regulation at the post-translational level. Also regulation at the level of differential splicing is suggested by the fact that several Aspergillus EST databases carry a considerable fraction of clones in which in frame intron sequences are retained.

Clonal variation in maximum specific growth rate and susceptibility towards antimicrobials.

To examine associations between growth rate within bacterial populations and survival patterns following treatment with antimicrobial agents. Time survival data were generated for the inactivation of Escherichia coli populations, grown as batch and continuous cultures, exposed to ciprofloxacin, benzalkonium chloride and tetracycline. Time-survivor plots were biphasic. Surviving cells were collected and immediately re-exposed to agent or were regrown and then re-exposed. Survivors were resistant to immediate challenge with any of the treatment agents. This resistance was lost on regrowth suggesting that survival reflects an expressed phenotype within a subset of the culture (persisters) rather than individual resistant clones or nonspecific quenching of the test agent. The fraction of persisters increased with decreasing growth rate when cultures were prepared in continuous culture. Clonal growth rates within populations were determined by culture of individual cells within microtitre plate wells. The fraction of clones, in batch cultures, growing maximally at rates below the apparent threshold for susceptibility to the test agents was sufficient to explain the results of continuous culture experiments. The presence of persisters in populations of bacteria relate to small subset of cells that are growing only slowly or are metabolically quiescent.

Discrimination between Translesion Synthesis and Template Switching during Bypass Replication of Thymine Dimers in Duplex DNA

The goal of this study was to determine whether bypass replication occurs by translesion synthesis or template switching (copy choice) when a duplex molecule carrying a single cis,syn-cyclobutane thymine dimer is replicated in vitro by human cell extracts. Circular heteroduplex DNA molecules were constructed to contain the SV40 origin of replication and a mismatch opposite to or nearby the dimer. Control molecules with only the mismatch were also prepared. Heteroduplexes were methylated at CpG islands and replicated in vitro (30 min). Following bisulfite treatment, the nascent DNA complementary to the dimer-containing template was distinguished from the other three strands by methylation-specific polymerase chain reaction. Cloning and sequencing of polymerase chain reaction products revealed that 80-98% carried the sequence predicted for translesion synthesis, with two adenines incorporated opposite the dimer. The fraction of clones with sequence predictive of template switching was reduced when extracts deficient in mismatch repair or nucleotide excision repair activities were used to replicate the heteroduplex molecules. These results support the conclusion that lesion bypass during in vitro replication of duplex DNA containing thymine dimers occurs by translesion synthesis.

Clustering of spore-specific genes in Aspergillus nidulans.

We have investigated the chromosomal organization of genes that are expressed specifically in the asexual spores (conidia) of the Ascomycete fungus Aspergillus nidulans, using two experimental approaches. In the first, 30 different recombinant clones, containing long nuclear DNA inserts and at least one spore-specific gene, were selected randomly. The total number of spore-specific genes present in each clone was then determined by RNA blot analysis. In the second approach, several chromosomal recombinant DNA libraries, having average insert lengths ranging from 1 to 15 kilobases, were constructed. The fraction of clones in each library having one or more spore-specific poly(A)+RNA-coding regions was then determined by colony or plaque filter hybridization with radiolabeled, spore-specific, complementary DNA. The results from these experiments were compared to statistical predictions based on the assumption that the spore-specific genes are randomly distributed in the Aspergillus genome. In both cases, the experimental values deviated significantly from the predicted values, demonstrating that the spore-specific genes are nonrandomly arranged in the genome. Rather, they appear frequently to occur in tightly linked clusters.

Recognition of polymorphic H-2 domains by T lymphocytes. I. Functional role of different H-2 domains for the generation of alloreactive cytotoxic T lymphocytes and determination of precursor frequencies.

In the present communication, the repertoire of alloreactive cytotoxic T lymphocytes (CTL) clones was quantitatively investigated by limiting dilution analysis and by target inhibition with a panel of monoclonal antibodies (mAb). These mAb have previously been shown to define two distinct alloantigenic domains, A and B, on the H-2Kk molecule. The Poisson distribution analysis of H-2Kk-specific CTL clones generated in a limiting dilution system revealed three CTL populations with different precursor frequencies. The high frequent population is suppressed by an unknown suppressive mechanism that allows less frequent CTL populations to become visible. Target inhibition studies with a panel of Kk-specific mAb showed that these CTL populations differ not only in their precursor frequency but also in their specificity for different H-2 epitopes on the Kk molecule. Thus clones of the high frequency population are almost exclusively specific for determinants within domain A. In contrast, the low frequency population displays predominant specificity for determinants of domain B, while the population with medium frequency is blocked equally well by mAb against either domains A or B. Each mAb blocked only a fraction of clones indicating that each CTL subpopulation may consist of a large number of clonotypes with specificity for different H-2 epitopes. The data suggest that CTL recognize basically the same polymorphic domains on the H-2Kk molecule defined by antibodies, and they show that regulatory mechanisms determine the expressed repertoire in CTL populations.