Small Fraction Research Articles

Phosphorus Speciation, Migration and Transformation in Seawater and Sediments and Potential Role in Starfish Outbreaks of the Xisha Islands, Northern South China Sea

AbstractPeriodic outbreaks of crown‐of‐thorns starfish have led to severe coral reef degradation, with one hypothesized cause being eutrophication. Phosphorus (P) is one of the driving factors for eutrophication, but researches on the spatiotemporal distributions of P in coral reefs are limited, impeding our understanding of the P cycling in coral reefs and its correlation with starfish outbreaks. This study undertook an analysis of various P species, migration and transformation in seawater, sediments, and crown‐of‐thorns starfish within the coral reefs of the Xisha Islands, northern South China Sea. The results show that in seawater, P predominantly existed in the dissolved phase, with organic P constituting the largest fraction (>67%). Conversely, in sediments, P primarily existed as inorganic form (43%−95%), with calcium‐bound P comprising the majority (26%−46%). Notably, exchangeable P accounted for a relatively smaller fraction (9%−20%) but played a significant role as a source of P released from sediments into seawater (0.01−0.17 mmol m−2 hr−1). During starfish outbreaks, starfish (1,000 individuals per hectare) assimilated P from seawater via phytoplankton or corals, resulting in substantial accumulation of both organic and inorganic P in their tissues (69−315 μmol g−1). Meanwhile, starfish excretion released P back into the seawater, which contributes to the migration and transformation of various P forms. Historical data also show a close relationship between P content and starfish density. These findings highlight the interactions between starfish and P cycling within coral reefs, and provide valuable insights into conservation and restoration on coral reefs, especially those severely affected by starfish outbreaks.

PI3K/PTEN/mTOR pathway dynamic tracking and prognostic value in HR+/HER2− BC patients with residual disease after neoadjuvant chemotherapy: a cohort study

AimsHormone receptor-positive (HR)+/HER2− breast cancer (BC) is highly heterogeneous, with PI3K/PTEN/mTOR pathway alterations emerging as possible players within this complexity. We longitudinally tracked PI3K/PTEN/mTOR pathway dynamics from baseline biopsy to...

Molecular investigation of MEFV gene polymorphisms among patients with familial mediterranean fever-like symptoms.

The diagnosis of familial Mediterranean fever (FMF) is primarily based on clinical standards. The purpose of this study was to investigate the relevance of Mediterranean fever (MEFV) genetic testing in the diagnosis of FMF as well as to identify the most frequent variant alleles and their relationship to clinical symptoms in Egyptian patients. Egyptian patients with a clinical suspicion of having FMF were studied in order to determine MEFV genotypes. Each patient was meticulously evaluated through an extensive collection of their medical history, a thorough clinical examination, and a series of laboratory tests, encompassing CBC, ESR, and CRP measurements. The MEFV variant screening procedure included the use of reverse dot blot hybridization. The average age of our patients when they were given a diagnosis was 22.8 ±1.404 years old. The predominant clinical manifestations identified were abdominal pain, fever, and arthralgia. Molecular interrogation of the MEFV gene unveiled that a significant proportion of the cohort, constituting 72 individuals (60%), displayed heterozygosity, whereas a smaller fraction, comprising 12 subjects (10%), demonstrated homozygosity and an equivalent number (10%) exhibited compound heterozygosity. Pertaining to the distribution of allele variants, E148Q emerged as the most prevalent, succeeded by M694I, accounting for 12.5% of the cases, and M680I (G/A), representing 10.41%. This notable prevalence of heterozygous genotypes among the Egyptian demographic, preliminarily identified as potential FMF cases, underscores the imperative for molecular diagnostics to enhance the precision of FMF identification.

Iron chelation capacity and prediction of peptide binding modes identified in California red worm hydrolysates and effects on iron bioavailability in differentiated Caco-2 cells

Metal-chelating peptides represent an alternative for overcoming iron deficiencies, a common nutritional disease affecting populations worldwide. This study explored the iron-chelating activity of California red worm hydrolysates (WH) and its fractions. WH was obtained by hydrolysis with Alcalase 2.4 L and fractionated using a ceramic membrane with molecular weight cutoff 3 kDa. Both the complete hydrolysate and its fractions were assessed for their in-vitro iron-chelating activity and their ability to improve iron bioavailability through ferritin formation by differentiated Caco-2 cells assay. Finally, peptides in the fraction with the highest activity were sequenced by LC-MS/MS analysis and molecular docking was performed to elucidate the chelation mechanism. The findings reveal that the smallest fraction (F < 3 kDa) exhibits the most potent iron-chelating activity with IC50 value like carnosine. Moreover, in intestinal-like differentiated Caco-2 cells, this fraction enhances iron bioavailability in a remarkable 77.9% in comparison to FeSO4 alone. On the other hand, the peptide SLLDDRLDEK identified in this fraction presents the lowest value of affinity energy (−1.5 kcal/mol) and exhibits specific interactions with iron, allowing iron ions to be trapped within its structure. These results underscore the potential of F < 3 kDa fractions from WH as promising candidates for increasing iron bioavailability and addressing iron deficiency and related health concerns.

Progressive heterogeneity of enlarged and irregularly shaped apicoplasts in P. falciparum persister blood stages after drug treatment.

Morphological modifications and shifts in organelle relationships are hallmarks of dormancy in eukaryotic cells. Communications between altered mitochondria and nuclei are associated with metabolic quiescence of cancer cells that can survive chemotherapy. In plants, changes in the pathways between nuclei, mitochondria, and chloroplasts are associated with cold stress and bud dormancy. Plasmodium falciparum parasites, the deadliest agent of malaria in humans, contain a chloroplast-like organelle (apicoplast) derived from an ancient photosynthetic symbiont. Antimalarial treatments can fail because a small fraction of the blood stage parasites enter dormancy and recrudesce after drug exposure. Altered mitochondrial-nuclear interactions in these persisters have been described for P. falciparum, but interactions of the apicoplast remained to be characterized. In the present study, we examined the apicoplasts of persisters obtained after exposure to dihydroartemisinin (a first-line antimalarial drug) followed by sorbitol treatment, or after exposure to sorbitol treatment alone. As previously observed, the mitochondrion of persisters was consistently enlarged and in close association with the nucleus. In contrast, the apicoplast varied from compact and oblate, like those of active ring stage parasites, to enlarged and irregularly shaped. Enlarged apicoplasts became more prevalent later in dormancy, but regular size apicoplasts subsequently predominated in actively replicating recrudescent parasites. All three organelles, nucleus, mitochondrion, and apicoplast, became closer during dormancy. Understanding their relationships in erythrocytic-stage persisters may lead to new strategies to prevent recrudescences and protect the future of malaria chemotherapy.

Effect of individual and synergistic alloying of In and Ni on microstructure, phase stability and thermal properties of lead-free Sn-0.7Cu solder

ABSTRACT The study explores the individual and synergistic effect of alloying indium (In) and nickel (Ni) with Sn-0.7 wt.% Cu solder on microstructure and thermal properties. Solders consist of β-Sn phase matrix and Cu6Sn5 intermetallic phase. In dissolves within β-Sn, while Ni substitutes Cu atoms of Cu6Sn5 forming (Cu,Ni)6Sn5. Alloying either In or Ni with Sn-0.7Cu lowers solidus and liquidus temperatures of the alloys, with a greater reduction in the case of In. Synergistic alloying of In and Ni with Sn-0.7Cu leads to a widening of 93%. Smaller fraction and localised presence of Cu6Sn5 in In-containing alloys resulted in dual-peaked grain size distribution. In the case of Ni, a fraction of (Cu,Ni)6Sn5 increased, generating more interfaces for nucleating β-Sn grains and eventually causing grain refinement. An increment in the fraction of low-angle grain boundaries (LAGBs) was observed in both alloying cases. The synergistic effect of In and Ni yields a more uniform grain size and lesser LAGBs.

Rare earth elements and yttrium (REY) in fjord waters: Comparison between seawater in the Trondheimfjord (Norway), its local riverine REY sources and the North Atlantic

The rare earth elements and yttrium (REY) are critical resources increasingly released into the environment due to their pivotal role for an ever-growing number of high-tech products and processes. Fjords, worldwide and particularly in Norway, are not only of high importance for biodiversity but they also have great economic value. Knowledge on the distribution of REY in Norwegian coastal and riverine waters is, however, surprisingly scarce. We here report REY data for water samples from depth profiles from ten stations in the Trondheimfjord, one of Norway’s largest fjords, several Norwegian rivers, and two wastewater treatment plants in Trondheim.Our results show that water from different locations in the Trondheimfjord yield similar REY concentrations that correlate well with dissolved organic carbon. The deepest sample at each station shows the lowest REY concentrations. The shale-normalised (SN) REY patterns of the fjord waters resemble those of North Atlantic seawater, but can be distinguished from open-ocean water by the smaller fractionation between light and middle REY (PrSN/TbSN ≥ 0.5). Stations in the vicinity of a river mouth show considerably higher REY concentrations at shallow depths. The respective REYSN patterns resemble the typically flat patterns of boreal rivers that are often rich in nanoparticles and colloids (NPCs). The REYSN patterns of the four rivers investigated (Nidelva, Orkla, Gaula, Stjørdalselva) show the features of the shallow(er) fjord water samples but have even higher REY concentrations. Ultrafiltration (< 1 kDa) data for the Nidelva corroborate that the typical “REYSN seawater signature” is in fact already present in freshwater where it is, however, usually hidden by the REY associated with NPCs. The local wastewater treatment plants release anthropogenic Gd (from contrast agents used in magnetic resonance imaging) into the Trondheimfjord, but this signal is immediately diluted and thus is not observed in the REYSN patterns of the fjord water. However, our results in general suggest that the slightly elevated Gd/Tb ratios observed in almost all fjord waters relative to North Atlantic marine water may rather be due to the presence of anthropogenic Gd in the southern North Sea and the Baltic Sea, corroborating that anthropogenic Gd can be applied as a sensitive far-field watermass tracer.

Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm

ObjectiveThis study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from the taxonomically diverse DNA background of next-generation sequencing procedures.DesignWe...

Kinetic Isotope Effects During Reduction of Fe(III) to Fe(II): Large Normal and Inverse Isotope Effects for Abiotic Reduction and Smaller Fractionations by Phytoplankton in Culture

AbstractIron stable isotopes (δ56Fe) are a useful tool for studying Earth processes, many of which involve redox transformations between Fe(III) and Fe(II). Here, we present two related experimental efforts, a study of the kinetic isotope effects (KIEs) associated with the reduction of Fe(III)‐ethylenediaminetetraacetic acid (EDTA) to Fe(II), and measurements of the biological fractionation of Fe isotopes by phytoplankton in culture. Reductants tested were ascorbate, hydroxylamine, Mn(II), dithionite, and photoreduction at pH between 5 and 9 and temperatures from 0 to 100°C. Isotope fractionations were very large, and included both normal and inverse KIEs, ranging from −4‰ to +5‰. Experiments were reproducible, yielding similar results for triplicate experiments run concurrently and for experiments run weeks apart. However, fractionations were not predictable, without a clear relationship to reaction rate, temperature, pH, or the reductant used. Acquisition of Fe by eukaryotic phytoplankton also often involves the reduction of Fe(III) to Fe(II). Several species of diatoms and a coccolithophore were tested for Fe isotope fractionation in culture using EDTA, NTA, and DFB as Fe(III) chelating ligands, yielding fractionations from −1.3‰ to +0.6‰. Biological isotope effects were also unpredictable, showing no clear relationship to species, growth rate, or Fe concentration. Variability in Fe isotope fractionation observed in culture may be explained in part by the sensitivity of KIEs. This work has implications for the industrial purification of isotopes, interpretation of natural δ56Fe, and the use of Fe isotopes as a tracer Fe source and biological processes in the ocean and other natural systems.

Optimization of Dual Antiplatelet Therapy in Pakistani Patients Undergoing PCI: A Strategy to Minimize Bleeding Risks and Improve Outcomes

Background: Percutaneous Coronary Intervention (PCI) is essential for treating coronary artery disease. The use of Dual Antiplatelet Therapy (DAPT) is crucial to prevent thrombotic complications but presents bleeding risks. This challenge is accentuated by the variability in genetic, demographic, and regional factors, particularly in Pakistan, where there is a high prevalence of cardiovascular diseases. Objective: To optimize DAPT strategies for Pakistani patients undergoing PCI by minimizing bleeding risks while ensuring therapeutic efficacy, aiming to pioneer personalized cardiovascular care. Methods: A retrospective cohort analysis was conducted at Lady Reading Hospital, Peshawar, involving 500 patients who underwent PCI and received DAPT from January 1, 2023, to January 1, 2024. Comprehensive data collection included patient demographics, clinical histories, specifics of PCI procedures, and outcomes of bleeding and thrombotic events, through a detailed review of medical records. Results: The cohort predominantly consisted of males (70%), with an average age of 58 years. Most patients (96%, n=480) were prescribed aspirin and clopidogrel, while a smaller fraction (4%, n=20) received aspirin and ticagrelor. Compliance was high, with 90% adherence. Bleeding occurred in 10% of the cohort (n=50), with major bleeds necessitating hospitalization in 4% (n=20). Thrombotic events were noted in 3% of patients (n=15). Conclusion: The study underscores the importance of personalized DAPT regimens that address individual risks and regional healthcare challenges in Pakistan. Tailored approaches are essential for optimizing treatment efficacy and safety, advocating for advanced, nuanced cardiovascular care practices.

OGLE-2023-BLG-0836L: The sixth microlensing planet in a binary stellar system

Aims. Light curves of microlensing events occasionally deviate from the smooth and symmetric form of a single-lens single-source event. While most of these anomalous events can be accounted for by employing a binary-lens single-source (2L 1S) or a single-lens binary-source (1L2S) framework, it is established that a small fraction of events remain unexplained by either of these interpretations. We carried out a project in which data collected by high-cadence microlensing surveys were reinvestigated with the aim of uncovering the nature of anomalous lensing events with no proposed 2L 1S or 1L 2S models. Methods. From the project we found that the anomaly appearing in the lensing event OGLE-2023-BLG-0836 cannot be explained by the usual interpretations, and we conducted a comprehensive analysis of the event. From thorough modeling of the light curve under sophisticated lens-system configurations, we arrived at the conclusion that a triple-mass lens system is imperative to account for the anomalous features observed in the lensing light curve. Results. From the Bayesian analysis using the measured observables of the event timescale and angular Einstein radius, we determined that the least massive component of the lens has a planetary mass of 4.36−2.18+2.35 MJ. This planet orbits within a stellar binary system composed of two stars with masses 0.71−0.36+0.38 M⊙ and 0.56−0.28+0.30 M⊙. This lensing event signifies the sixth occurrence of a planetary microlensing system in which a planet belongs to a stellar binary system.

A case for stronger integration of physical landscape processes in conservation science and practice.

I argue that the dynamic nature of contemporary, landscape-shaping (geomorphic) processes deserves more consideration in conservation science and practice. In an analysis of a sample of fundamental terms related to geomorphology and area-based conservation in the Web of Science, I found that the terms co-occurred in <2% of the analyzed entries (titles, abstracts, and keywords) from 2000 to 2020. This result is indicative of the rather peripheral attention that, more broadly, landscape-shaping processes seem to receive in the conservation literature. Among conservation scientists and practitioners, landforms that define the physical structure of habitat are often perceived as largely static, whereas the consideration of their dynamic adjustments to geomorphic processes is often limited to extreme events. I use examples derived from river-floodplain environments to illustrate strong, multifaceted, and reciprocal interactions between biota and various erosional and depositional processes. These ubiquitous interdependencies clearly demonstrate that geomorphic processes are an integral part of ecosystem dynamics at time scales relevant for conservation. Crucially, erosional and depositional processes modulate many environmental impacts of past and current anthropogenic activities. I conclude that the absence of a more explicit and widespread consideration of geomorphic processes in conservation science and practice is surprising and detrimental to their effectiveness. I call for bolstered efforts among the conservation and geoscience communities to better integrate landscape dynamics within the field of conservation. The rise of the ecosystem-based and social-ecological systems approaches to conservation and the growth of interdisciplinary geoscience branches (e.g., biogeomorphology, ecohydraulics, and geoconservation) will facilitate such an integration.

Unravelling variations: an examination of entry point selection in proximal femoral cephalomedullary nailing

BackgroundThe exact positioning of the cephalomedullary (CM) nail entry point for managing femoral fractures remains debatable, with significant implications for fracture reduction and postoperative complications. This study aimed to explore the variability in the selection of the entry point among trauma surgeons, hypothesizing potential differences and their association with surgeon experience.MethodsIn this prospective multicenter study, 16 participants, ranging from residents to senior specialists, partook in a simulation wherein they determined the optimal entry point for the implantation of a proximal femoral nail antirotation (PFN-A; DePuy Synthes) in various femora. The inter- and intra-observer variability was calculated, along with comprehensive descriptive statistical analysis, to assess the variability in entry point selection and the impact of surgeon experience.ResultsIn this study, the mean distance from the selected entry points to the calculated mean entry point was 3.98 mm, with a smaller distance observed among surgeons with more than 500 implantations (ANOVA, p = 0.050). Intra-surgeon variability for identical femora averaged at 5.14 mm, showing no significant differences across various levels of surgical experience or training. Notably, 13.6% of selected entry points would not allow a proper intramedullary positioning of the implant, thereby rendering anatomical repositioning unfeasible. Among these impossible entry points, a significant skew towards anterior placement was observed (70.6% of the impossible entry points), with a smaller fraction being overly lateral (27.5%) or medial (13.7%). On a patient level, the impossibility rate varied widely from 0 to 35% among the different femora examined, with a significantly higher rate seen in younger patients (mean age 55.02 versus 60.32; t-test for independent samples, p = 0.04).ConclusionsSignificant variations exist in surgeons’ selection of entry points for proximal femoral nailing, underscoring the task’s complexity. Experience does not prevent the choice of unfeasible entry points, emphasizing the inadequacy of a universal approach and pointing towards the necessity for a patient-specific strategy for improved outcomes.Trial registration number: DRKS00032465.

The use of drama in A Level chemistry: a study into the effects of simulation-role-play on the quality of learning of organic reaction mechanisms

ABSTRACT Background Much of the research into the use of drama in science education has been qualitative, with its primary focus being on its affective value amongst students aged 6–14 years, with a smaller fraction on effectiveness in terms of academic achievement and understanding of chemistry amongst older school students (16–18 years). Purpose This article reports on a study that compared the effectiveness of drama, as a pedagogy, with a didactic practice-examinations-questions-based approach on students’ understanding of chemistry organic reaction mechanisms as measured by examination question scores. Sample Data were collected in seven 11–18 schools and a Further Education (FE) college in England, with a total of 236 students, aged 16–18 years, studying Advanced (A) Level chemistry. Each institution had two different classes studying chemistry concurrently. Design and methods The research was a quasi-experimental intervention with one class of A Level chemistry students in each institution being taught an aspect of organic reaction mechanisms using drama and the second, non-drama, class being taught the same material using practice examination questions. Post-intervention, all students completed previously unseen A Level examination questions and, in one phase of the study, a diagnostic question designed to probe deeper understanding. The responses were subject to statistical analysis. Results In all cases there were no statistically significant differences between the test scores of the two groups for the answers to the examination questions. However, answers to a diagnostic question, probing deep level understanding, showed a statistically significant difference between the two groups in favour of the drama group. Conclusions Whilst drama is at least as effective as the use of practice examination questions in the teaching and learning of organic reaction mechanisms it was statistically significantly more effective in terms of the development of deeper level conceptual understanding.

Assessment of handling practices for maize by farmers and marketers in food-insecure regions of Western Honduras

The objective of this study was to understand the maize production chain in the Republic of Honduras, and to identify potential obstacles hindering grain end-quality. Seventy-one municipalities across six departments of Western Honduras were surveyed: Copán, Intibucá, La Paz, Lempira, Ocotepeque, and Santa Bárbara. A total of 871 surveys were collected, out of which 725 were from rural areas and 146 from urban areas. The sampling design reflected population density and population-based indicators from USAID's Feed the Future initiative, such as poverty level and prevalence of underweight non-pregnant females between the ages of 15 and 49. Further, indicators associated with underdevelopment in children were also considered. Survey instruments designed for either maize farmers or maize marketers were used to collect data including seed source, type planted, intercropping, time of harvest, drying and storage practices, quality control, and consumption patterns. Farmers preferred to plant criolla (native) maize (81–96%), although non-native varieties were also grown and consumed (3–13%). Following harvest, sun drying is the most used method (14–40%) for moisture control. Farmers reported maize spoilage resulting primarily from inadequate drying and pest damage (56–82%). Although aware of this, up to 28% of the producers reported not performing preventive grain inspections in the course of storage. Maize marketers typically sourced their grain within the department (33–71%), with a smaller fraction (0–8%) also obtaining maize from other departments or neighboring countries. Mirroring farmers, visual quality checks by marketers occurred primarily at initial storage (36–69%) and decreased in frequency as storage time lengthened. Given that both studied groups of farmers and marketers continue to rely on traditional practices, and corrective rather than preventive measures, the likelihood of low-quality product and risk for mycotoxin contamination is exacerbated. Based on these findings, achieving food security for the region of study will require a transformation in pre- and post-harvest handling practices.

Current Therapeutic Strategies for Chagas Disease

Abstract: Trypanosoma cruzi, the parasite that causes Chagas disease, can only be cured with one of two drugs, benznidazole or nifurtimox. The main disadvantages of these drugs include their ineffectiveness outside of the acute or early infection phase, their unpleasant effects, and the parasite's tolerance to their activities. On the other hand, several institutions and research groups have been working on a number of ways that can help find a solution to the problem. These strategies have evolved over the last few years. Several examples of such advancements include the utilization of combination therapy, the repurposing of current treatments, and the change of dosages for traditional drugs. Research has also been conducted on antiparasitic plants and the substances that may be obtained from them, and it makes use of existing knowledge gathered through medical procedures. Some works have studied the parasite in order to identify important genes that have the potential to be used as therapeutic targets in the development of novel targeted medications. Even though a lot of these studies have shown promising results, only a small fraction of them make it to the clinical testing phase of the study. Institutions and research organizations should be rewarded for coordinating their efforts and addressing all areas of drug development, given their resources and information. Last but not least, distributing this information will result in novel Chagas disease therapies, which would assist impacted populations.

Abstract 6147: Genome-wide association study identifies new genetic susceptibility loci for multiple primary cancers

Abstract Objectives: Genetic susceptibility is thought to contribute to the development of multiple primary cancers (MPC), often called secondary cancers. Although rare variants contribute to risk, these only account for a small fraction of MPC cases. The contribution of common variants to risk is unknown. Methods: To identify common genetic variants associated with the risk of MPC, we conducted a trans-ancestry meta-analysis of genome-wide association studies (GWAS), including 7,360 MPC cases and 138,684 controls from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and UK Biobank (UKBB). Association analyses were performed separately by genetic ancestry, genotype platform, and study, adjusting for age, sex, and principal components, and the results were meta-analyzed together using a fixed effects model. Genome-wide SNP heritability was estimated using GCTA. Pathway and functional enrichment analyses were conducted to gain insights into potential biological mechanisms underlying discovered loci. Results: We identified one novel locus at chromosome 3q26.2 (LRRC34, rs7621631) that was associated with MPC risk (P=1.16x10-8). Variants in this region have been previously associated with telomere length, suggesting a possible underlying mechanism. In sex-stratified analyses, we identified an additional locus at chromosome 12q24.33 (intergenic, rs10466868) associated with MPC in men (P= 7.76x10-8), but not women. Although the risk associated with these two discovered loci was small, the genome-wide SNP heritability was estimated to be 12%, suggesting that there are likely more common variants to be discovered for MPC risk. Conclusions: Our study demonstrates that common genetic variation contributes to the risk of multiple primary cancers and suggests additional loci are likely to be identified with larger studies. Citation Format: Shisi He, James Perry, Shengchao Li, Braxton D. Mitchell, Yuji Zhang, Shuo Chen, Laura Beane-Freeman, Kathryn Hughes Barry, Sonja I. Berndt. Genome-wide association study identifies new genetic susceptibility loci for multiple primary cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6147.

Abstract 1609: Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases

Abstract Non-small cell lung cancer (NSCLC) is a highly complex disease, characterized by extensive genomic heterogeneity and dynamic evolution under therapeutic pressure. This evolution can lead to alterations in the antigens expressed by cancer cells, thereby influencing the T cell repertoire (TCR) as T cells expand in response to foreign antigens. Despite the central role of TCR in cancer progression and treatment response, only few studies have investigated the temporal and spatial changes in the TCR repertoire. In this study, we delve into the role of the TCR repertoire in metastatic progression in NSCLC. We conducted TCR sequencing of multiregion primary tumors, normal-adjacent tissues, and post-mortem metastases sampled from a cohort of 22 patients enrolled in the TRACERx and PEACE studies. Our findings reveal that primary tumor regions and normal-adjacent tissues exhibit similar fractions of expanded clonotypes. However, a higher proportion of expanded intratumoral TCRs were privately expanded in the tumor samples, suggesting a unique TCR landscape within the tumor microenvironment. The TCR repertoire across multiregion primary tumor samples was largely homogenous, with most expanded clonotypes shared across at least two regions. However, only a small fraction of these clonotypes were tracked in metastases, indicating a significant shift in the TCR repertoire during metastatic progression. Notably, the expanded clonotypes that persisted over time from early to late stage disease were significantly enriched for clonotypes ubiquitously expanded in the primary tumor across all regions. This was not shown to be associated with an increased likelihood of generation via VDJ recombination, suggesting a tumor-specific immune response. The expanded TCR repertoire in the postmortem metastases clustered mainly by anatomical site, suggesting an immune response driven by tissue-resident T cells. Moreover, we found a significant positive correlation between repertoire dissimilarity and genomic distance, suggesting that T cell clones track with tumor clones across spatial sites within patients. Our study demonstrates the significant spatiotemporal dynamics of the TCR repertoire during the metastatic progression of NSCLC, orchestrated by both tissue-resident T cells and the genomic evolutionary trajectory of tumors. Such an exploration could provide valuable insights to inform future strategies for immunotherapy treatments and enhance clinical monitoring of patients. Citation Format: Corentin Richard, Sonya Hessey, Cristina Naceur-Lombardelli, Selvaraju Veeriah, Gayathri Nageswaran, Crispin Hiley, Sergio Quezada, Benny Chain, TRACERx and PEACE Consortia, Charles Swanton, Mariam Jamal-Hanjani. Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1609.

Abstract 6258: Inference of gene expression using fragmentation patterns from targeted high-depth sequencing of cell-free DNA

Abstract Cell-free DNA (cfDNA) circulating in blood plasma arises primarily from cellular chromatin fragmentation and release due to cell death. Studies have demonstrated that the assessment of fragmentomic features of cfDNA enables gene expression inference and tissue-of-origin classification with potential applications for noninvasive cancer detection. However, due to low depth of coverage of sites of interest, current whole genome sequencing (WGS) methods have not been able to infer expression of individual genes or limited gene sets. Therefore, we developed a targeted sequencing approach that enables individual gene expression inference from cfDNA fragmentation patterns based on transcriptional start-site gene activation probability (TSS-GAP). To assess the sensitivity of this method for cfDNA-inferred gene expression profiling, we applied TSS-GAP to blends of micrococcal nuclease (MNase)-digested DNA from a cancer cell line (LS180) and sorted peripheral blood mononuclear cells (PBMC), with LS180 DNA at varying concentrations (0.1-10%). This enabled the determination of the limit of detection (LoD), relative to healthy donor background levels, on the basis of the genes’ activation probabilities (TSS-GAP scores). We found 936 genes with high inferred expression in the LS180 cancer cell line and low inferred expression in non-cancer samples (i.e. CD4, CD14, and plasma cfDNA from 4 healthy donors) and used those for healthy donor background and LoD assessment. Using these gene-level background values as cutoffs, blends were assessed to determine the lowest blend level at which expression of the gene was able to be differentiated from background. Out of the 936 genes, 326 (34.8%) were detectable at a blend level of 0.1%, 59 (6.3%) at 0.3%, 31 (3.3%) at 1%, 19 (2.0%) at 3%, and 39 (4.2%) at 10%. In total, 416 genes could be detected by TSS-GAP at levels 1% of or lower above background, highlighting the potential of our method for detecting expression of certain genes even from a small fraction of cells contributing cfDNA to liquid biopsy samples. Further expansion of this work could consider the utility of such a method for circulating tumor DNA (ctDNA) detection, cfDNA tissue-of-origin classification, and deconvolution of cell types contributing to cfDNA found in blood. Citation Format: Emily Leff, Alexander Tseng, Victoria Cheung, Ehsan Tabari, Kimberly Walter, Alex Lovejoy, Cheng-Ho J. Lin. Inference of gene expression using fragmentation patterns from targeted high-depth sequencing of cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6258.

On some silverfish taxa from the Cape York region of northern Australia (Zygentoma: Lepismatidae: Ctenolepismatinae)

ilverfish (Zygentoma) are an ancient, but poorly studied group of primitively wingless insects. Species definition based on morphology alone is complicated by variations arising from the continuous moulting, even after reaching sexual maturity. In recent studies the use of molecular data has supported the identification of consistent morphological character traits, however only a small fraction of the species have been investigated. Eight species of the large silverfish genus Acrotelsella, collected by the first author from the Cape York Peninsula of northeastern Australia, are described and named as new species. Molecular data (COI and 28S) are presented that reinforces previous suggestions that the genus will eventually need to be split into two.