Pairs Of Sequences Research Articles

Abstract 2062: Identification of functional MAIT-specific TCRs using MR1 dCODE Dextramer® reagents and evaluating antigen presentation

Abstract Objectives: To support TCR discovery and enable evaluation of TCR target expression on the surface of cells, we have established a streamlined workflow allowing TCR Discovery, validation and evaluation of MHC-antigen expression on target cells. As proof of concept, MR1 dCODE Dextramer® reagents were used to identify antigen-specific MAIT cells using single-cell sequencing, TCR sequences were extracted from the resulting data and then cloned and expressed as TCR monomers. The specificity of the TCRs was subsequently validated as TCR Dextramer® reagents and used to evaluate target MHC-peptide presentation on cell surface. Methods: Mixed PBMC samples from three healthy donors were stained with antibodies targeting relevant phenotypic markers as well as MR1 dCODE Dextramer® reagents carrying the MAIT cell-specific ligand 5-OP-RU. Following staining, sorting, and partitioning on a BD Rhapsody™ Single-Cell Analysis System, the cells underwent sequencing for a characterization of gene and surface marker expression as well as paired alpha-beta TCR sequences. Single alpha and beta chains were individually expressed, refolded together and purified. Refolded TCR monomer functionality was validated using an artificial cell assay. The functional TCRs can be multimerized on a Dextramer® backbone and used to evaluate expression of target on cell surface. Results: The majority of the identified CD161+ MAIT cells (~70%) expressed typical TCRs consisting of TRAV1-2 and TRAJ33 as well as TRBV6/20, TRBD1/2, and TRBJ2 gene segments. Three alpha-beta TCR sequences were selected: Two TCRs having common TRAV+TRAJ, TRBV+TRBJ combinations and one having a rare TRAV+TRAJ one. TCR alpha and beta chains were successfully expressed for all selected TCRs but only 2 TCRs showed a correctly refolded TCR as demonstrated by proper recognition of MR1/5-OP-RU. Based on these two functional TCRs, TCR Dextramer® reagents were generated and used to evaluate expression of target antigen on cell surface. Conclusion: We demonstrate a workflow allowing: (i) Identification of MAIT cells and their corresponding TCR sequences. (ii) Generation of soluble TCR molecules based on the identified sequences and validation of their specificity. (iii) Generation of TCR Dextramer® reagents allowing identification of target expression on surface of cells. This workflow is also useful for identification of other antigen-specific T cells and creates a new tool for evaluation of antigen-expression by MHC on surface of cells. By combining the high sensitivity of dCODE Dextramer® technology with TCR sequencing and creation of TCR Dextramer® reagents, both low-affinity interactions and rare cell types can be detected and studied in unique detail. Citation Format: Kevin Lenogue, Bjarke Hansen, Kivin Jacobsen, Liselotte Brix, Thomas Holberg Blicher. Identification of functional MAIT-specific TCRs using MR1 dCODE Dextramer® reagents and evaluating antigen presentation [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 2062.

Abstract 27: A single amino acid mutated AFP specific T cell receptor uniting synergistic functionalities of CD4 and CD8 T Cells with no cross-activity

Abstract Background: Genetically engineered T cells with T cell receptor (TCR-T) cell therapy have shown great potential for cancer treatment by targeting tumor-associated antigens. Despite its success in treating various tumor types, such as synovial sarcoma, head and neck tumors, and cervical cancer, its application in liver cancer is limited. Alpha-fetoprotein (AFP), a highly expressed tumor-associated antigen in liver cancer, is an ideal target for TCR-T cell therapy. Although early human trials have confirmed the safety of AFP-targeting TCR-T products, their efficacy is still modest, highlighting the need for further research and development. Methods: We developed a robust strategy combining ex vivo stimulation and single-cell paired TCR sequencing to identify AFP-recognizing TCRs in liver cancer patients. To optimize TCR expression and minimize mispairing, we employed codon optimization and replaced the constant regions with murine counterparts. Furthermore, structural analysis guided the affinity optimization of the CDR3 region to enhance the antitumor function of the selected TCR. The anti-tumor efficacy of TCR-T cells was rigorously evaluated through in vitro cytotoxicity assays using the Real-Time Cell Analyzer (RTCA) system and in vivo antitumor assessment in immunodeficient mouse xenograft models. Antigen specificity, HLA restriction, and other potential toxicity were carefully evaluated in both in vitro and in vivo models. Results: We successfully cloned a highly effective TCR that recognizes the AFP158-166 epitope presented by HLA-A*0203. After sequence optimization, we further changed a single amino acid on the TCR vβ chain based on AI prediction. The expression and functionality of this TCR was significantly improved. When introduced into human T cells, the single amino acid mutated TCR demonstrated robust and specific anti-tumor activity in various models, including cultured tumor cells, patient-derived organoids, and mouse xenografts models. Notably, this TCR also redirected CD4 T cells to recognize tumor cells, induced the secretion of multiple cytokines, and maintained long-lasting anti-tumor effects. Our rigorous screening assays confirmed that the TCR showed no cross-reactivity with the human proteome or major HLA subtypes. Additionally, extensive preclinical safety assessments in tumor-bearing animals treated with ST08A01-AM14 TCR-T cells showed no significant safety concerns. Conclusion: In this study, we have developed an HLA-A*0203 restrict AFP158-166 specific TCR-T therapy, which exhibits exceptional anti-tumor effects while ensuring a favorable safety profile. The promising results support the further investigation against AFP-positive solid tumors in clinic. Citation Format: Chen-Song Huang, shudan Ou, Jun Li, Junjun Chu, Yanyan Han. A single amino acid mutated AFP specific T cell receptor uniting synergistic functionalities of CD4 and CD8 T Cells with no cross-activity [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 27.

Abstract 6600: Investigating molecular regulators of a dual identity state in lung adenocarcinoma

Abstract Lung adenocarcinoma (LUAD) is the largest subtype of lung cancer and is the most common cause of cancer related death. LUAD progression is driven by both genetic alterations and epigenetic changes that confer increased lineage plasticity and heterogeneity, but underlying mechanisms dictating cell identity in LUAD remain incompletely understood. The lineage defining transcription factors, NKX2-1 and FoxA1/2, coordinately maintain a pulmonary identity in LUAD. Recent work suggests that NKX2-1-positive (NKX2-1+) LUAD evolves from an alveolar-like state and adopts various disparate cell fates that drive progression, including “dual-identity” states, characterized by acquisition of gastrointestinal (GI) and pulmonary-like states in the same cell. Using sophisticated genetically engineered mouse models and 3D organoid cultures, we demonstrated that the gastrointestinal transcription factor HNF4α, which robustly marks the dual-identity state, is critical for growth in NKX2-1+ LUAD. We performed bulk RNA-seq and single cell RNA-seq in vitro and in vivo, and we found that loss of HNF4α alters the differentiation state of NKX2-1+ LUAD, causing cells to shed elements of their gastric identity in favor of alternate differentiation states. Using paired chromatin immunoprecipitation sequencing and RNA-seq in dual-identity organoids, we found that HNF4α can access and activate many of its canonical gastrointestinal target genes despite being aberrantly expressed in the lung, where it is typically epigenetically silenced early in development. Surprisingly, HNF4α also colocalizes with NKX2-1 and FoxA1/2 and binds at novel sites, suggesting that HNF4α acquires expanded activity in this state beyond its canonical roles. Together, our work unveils key insights into the mechanisms by which lineage defining transcription factors regulate cellular identity and growth in LUAD. Citation Format: Gabriela Fort, Soledad Camolotto, Rushmeen Tariq, Pengshu Fang, Katherine L. Gillis, Chris Stubben, Eric L. Snyder. Investigating molecular regulators of a dual identity state in lung adenocarcinoma [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 6600.

Abstract 6: Defining and therapeutically targeting a fusion-derived public neoantigen in desmoplastic small round cell tumor using T cell receptor gene therapy

Abstract Sarcomas are a heterogenous group of mesenchymal cell malignancies that are difficult to treat and often respond poorly to current immunotherapies. Approximately 30% of sarcomas are associated with oncogenic driver fusion proteins. Desmoplastic small round cell tumor (DSRCT) is a prototypical fusion-driven sarcoma defined by a pathognomonic EWSR1-WT1 fusion event. The resultant EWSR1-WT1 fusion protein contains a shared junctional amino acid sequence that is clonally conserved and significantly divergent from normal human proteins. Consequently, the EWSR1-WT1 fusion might yield a highly immunogenic shared, or public, neoantigen (NeoAg) that may serve as a target for novel immunotherapeutic approaches.Using a functional HLA-immunoprecipitation/mass spectrometry (HLA-IP/MS) screen, we identified a 9-amino acid peptide sequence derived from the junction of the most common EWSR1-WT1 fusion protein that is presented in the context of the prevalent HLA-A*03 and -A*11 alleles. We confirmed that HLA-A*03+ DSRCT cells physiologically present the same peptide sequence. Using fluorophore-conjugated HLA-multimers loaded with the HLA-IP/MS-derived fusion NeoAg, we identified a rare population of circulating NeoAg-specific CD8+ T cells in HLA+ DSRCT patients. Through antigen-directed clonal expansion, we discovered n=3 HLA-A*03-restricted and n=1 HLA-A*11-restricted fusion NeoAg-specific T cell clones and retrieved the paired TCRαβ gene sequences of their T cell receptors (TCRs) using 10x single-cell sequencing. Polyclonal CD8+ T cells transduced with candidate TCRαβ gene sequences robustly upregulated TNFα after coculture with HLA+/Fusion+ target cells but not HLA−/Fusion+ or HLA+/Fusion− control cells. Further, T cells expressing candidate TCRs, but not viral-protein-specific TCRs, lysed HLA+ DSRCT cells in vitro and controlled established DSRCT tumors in vivo. Finally, we discovered that one TCR was capable of cross HLA allele fusion NeoAg recognition and could lyse both HLA-A*03+ and -A*11+ DSRCT cells. These findings imply that a single TCR therapeutic could cover >36% of North American DSRCT patients.Collectively, our data establish for the first time that DSRCT cells present a junction-spanning fusion-derived neoantigen in the context of two prevalent HLA alleles that may be therapeutically targeted using TCR gene therapy. These data lay the foundation for first-in-human clinical translation of a T-cell based therapy targeting EWSR1-WT1. More broadly, these findings establish proof-of-principle that recurrent fusion proteins are an actionable source of immunogenic public NeoAgs, providing a framework for developing targeted immunotherapies for other fusion-driven malignancies. Citation Format: Lauren Banks, Hannah Arkin, Smita Chandran, Emily Slotkin, Madelyn Espinosa-Cotton, Neerav Shukla, Luc Morris, Marc Ladanyi, Andrew Kung, Martin Klatt, Christopher Klebanoff. Defining and therapeutically targeting a fusion-derived public neoantigen in desmoplastic small round cell tumor using T cell receptor gene therapy [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 6.

Abstract 1194: Understanding radiation and immunotherapy induced cell state shifts in the pancreatic tumor microenvironment

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with few effective treatment options. It is characterized by a highly desmoplastic tumor microenvironment and a paucity of dendritic cells, leading to low immune cell infiltration and poor outcomes with immunotherapy treatments that are highly effective in other cancers. In a recent pilot study, metastatic PDAC patients who had progressed on chemotherapy were treated with a combination of dual immune checkpoint blockade (ICB) therapy and radiation which resulted in an 18% overall response rate (ORR) and 29% disease control rate (DCR). This led to a phase 2 study in order to further test this combination with the goal of deep correlative analysis to understand the determinants of immunotherapy response and resistance. In this follow up there was a 3.6% ORR, 10.7% DCR, progression free survival (PFS) of 2.3 months, and a single patient with complete response. We collected 36 samples from 23 patients including primary pancreas tumor tissue and liver metastases, and 13 pairs of pre and on treatment biopsies. We performed single-nucleus and paired single-cell RNA and TCR sequencing on these samples to provide comprehensive insight into the cell types and biology present in this unique tumor microenvironment. Using supervised non-negative matrix factorization we have identified both previously established and novel gene programs that co-vary between cell types. Within the various tissue sites we have identified differing proportions of basal to classical tumor cell types and a distinct shift towards the classical state post-radiation. Of particular interest is a group of interferon related gene programs present within epithelial cell subtypes, C1QC+ and MHCII+ macrophages, and CD14+/CD16+ monocytes that indicate cell type specific responses to treatment. Focusing on the T cells, we found a distinct shift towards exhausted or proliferating states on treatment and using TCR sequencing data we have identified novel and expanding clones on treatment, largely consisting of those same cell subtypes. We also collected spatial transcriptomics data on a subset of patient samples, and analysis is ongoing to further confirm the cell type relationships identified in single-cell resolution data, along with spatial localization of basal to classical tumor states. This vast multimodal dataset allows us novel insight into the radiation and dual ICB induced cellular state shifts in the tumor microenvironment. Citation Format: Milan Parikh, Ryan Park, Aparna R. Parikh, Julie L. Koenig, Leon Pappas, Moshe Sade-Feldman, Lynn Bi, Nicole Carzo, Tarin M. Grillo, Islam Baiev, Olanike Asupoto, Irena Gushterova, Tom LaSalle, Anna Gonye, Emily Blaum, David P. Ryan, David T. Ting, Theodore S. Hong, Dana Pe'er, Nir Hacohen, Arnav Mehta. Understanding radiation and immunotherapy induced cell state shifts in the pancreatic tumor microenvironment [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 1194.

Abstract 8: Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors

Abstract Background: T cell receptor-engineered T cell (TCR-T) therapy has been studied as a high potential approach for cancer treatment. Beyond cell-surface tumor antigens, TCR-Ts can recognize HLA-presented intracellular epitopes which allows them to address a wide range of cancer-specific targets. Existing TCR-T therapies focus on a limited number of epitopes, many of which are restricted to HLA allele HLA-A*02:01. Identification of novel anti-tumor TCRs covering a broad range of HLA alleles is necessary to address unmet clinical needs. Natural T cells undergo thymic selection and present a favorable safety profile for mining such anti-tumor TCRs for therapeutic development. However, discovery of natural anti-tumor TCRs has been challenging due to i) the absence of high-throughput methods for identifying tumor-reactive TCRs in limited quantity human samples and ii) lack of sensitivity in detecting low frequency, naturally occurring tumor-reactive T cells. Methods: We developed TargetScape® as a part of our Deep Immunomics platform for efficient discovery of natural tumor-specific TCRs in healthy donors and cancer patients. Cells from blood and tissue samples were stained with metal-barcoded peptide-MHC tetramers, containing 500+ tumor-specific antigens, alongside metal-conjugated antibodies, allowing rapid identification and high dimensional phenotypic analysis of CD8+ T cells at the millions of cells scale. Single-cell sequencing revealed paired TCR sequences. Selected TCRs were introduced into luminescent Jurkat reporter cells for validation screening with peptide-pulsed targets and the relevant HLA restriction. TCRs of interest were further integrated into primary T cells and evaluated for their effector function. Results: We utilize our sensitive, high-throughput TargetScape® platform to detect and characterize putative cancer-specific TCRs from blood and tissue samples in frequencies as low as ~0.003% of total CD8+ cells. We have functionally validated over 100 TargetScape® derived TCRs with luminescent Jurkat reporters. Validated TCRs cover high prevalence HLA alleles and target a broad range of cancer antigen classes, including tumor associated antigens (TAA), Human endogenous retroviruses (HERVs), shared splice variants, and frameshift mutations. Several natural TCRs demonstrate recognition of low concentrations of peptide, indicating high functional avidity. Further evaluations of specificity and activity of TCRs of interest transduced into primary T cells are currently in progress. Conclusions: Our Deep Immunomics platform allows us to identify and confirm activity of novel, naturally-derived TCR candidates against therapeutically relevant cancer antigens presented on six common HLA alleles. These findings validate our discovery workflow leading to a portfolio of potential clinically relevant candidates that are currently under preclinical development. Citation Format: Hannah Fields, Juliana Velez Lujan, Kan Xing Wu, Natalie Epstein, Nazihah Beevi, Florence Chioh, Nicholas Tan, Neeraja Kulkarni, Noella Mukobo, Srikanthi R, Yovita Purwanti, Evan Newell, Alessandra Nardin, Michael Fehlings, Katja Fink, Daniel MacLeod. Deep Immunomics pipeline for discovery and validation of novel cancer-specific T cell receptors [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 8.

Abstract 910: Clinical inference and biological dissection of tumor ploidy and heterogeneity in cutaneous melanoma for immunotherapy response using deep learning

Abstract Background: Tumor ploidy and heterogeneity demonstrated to be pivotal in predicting immunotherapy response in cutaneous melanoma in several independent cohorts (Liu NatMed2019, Tarantino BioRXiv2022). Their estimation can guide more personalized and rational utilization of these immunotherapies. However, 1) the biology underpinning ploidy and heterogeneity is unknown; and 2) these findings were derived in patients using retrospective research tumor-normal paired whole exome sequencing which is not performed for clinical management. Methods: This study addresses this gap by employing deep learning models to predict these crucial markers using routinely available clinical assays, including H&E images. Attention-based computer vision models enable the identification of key morphological features in H&E slides. Segmentation of tumor tissue to perform automated masking, enhances ploidy inference.Moreover, biologically informed neural networks (P-Net, Elmarakeby Nature2021) uncover transcriptional and genomic features linked to ploidy and tumor heterogeneity. Our models are trained on publicly available data (e.g., Liu et al Nature Medicine 2019; TCGA SKCM) from melanoma cohorts and further validated in independent cohorts to ensure robustness. Results: We developed and validated automated tumor tissue masking, enabling the prediction of Whole Genome Doubling (WGD) from H&E Slides with an AUC > 0.75. Attention-based models identify distinct Tumor Microenvironment (TME) structures predictive of high tumor heterogeneity. P-Net application revealed the Calmodulin pathway, previously associated with regulating proliferation in cancer and targeted with chemotherapy, as intricately linked to high tumor heterogeneity, providing valuable insights into underlying mechanisms. Conclusion: In conclusion, our study strategically harnesses and integrates existing datasets to rigorously test, refine, and validate hypotheses concerning the biological and therapeutic implications of genomic heterogeneity and ploidy. Notably, our predictive models with automated tumor masking demonstrate a remarkable AUC >0.75 for biomarkers traditionally challenging to derive from clinical assays. This breakthrough opens avenues for novel therapeutic strategies targeting genomic heterogeneity and ploidy, providing a transformative potential to enhance patient care and outcomes. Citation Format: Marc Glettig, Giuseppe Tarantino, Tyler Aprati, Haitham Elmarakeby, David Liu. Clinical inference and biological dissection of tumor ploidy and heterogeneity in cutaneous melanoma for immunotherapy response using deep learning [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 910.

Tri-CLT: Learning Tri-Modal Representations with Contrastive Learning and Transformer for Multimodal Sentiment Recognition

Multimodal Sentiment Analysis (MSA) has become an essential area of research to achieve more accurate sentiment analysis by integrating multiple perceptual modalities such as text, vision, and audio. However, most previous studies failed to align the various modalities well and ignored the differences in semantic information, leading to inefficient fusion between modalities and generating redundant information. In order to solve the above problems, this paper proposes a transformer-based network model, Tri-CLT. Specifically, this paper designs Integrating Fusion Block to fuse modal features to enhance their semantic information and mitigate the secondary complexity of paired sequences in the transformer. Meanwhile, the cross-modal attention mechanism is utilized for complementary learning between modalities to enhance the model performance. In addition, contrastive learning is introduced to improve the model's representation of learning ability. Finally, this paper conducts experiments on CMU-MOSEI aligned and unaligned data, and the experimental results show that the proposed method outperforms the existing methods.

Molecular Characterization and Phylogenetic Analysis of Flightin Gene in Vespa basalis (Hymenoptera, Vespidae).

Flight is a complex physiological process requiring precise coordination of muscular contraction. A key protein in insect flight is flightin, which plays an integral role in the flight muscles. This research sought to evaluate the flight competence of the social wasp V. basalis by characterizing the molecular components involved. Our study focused on Vespa basalis, one of the most dangerous hornet species, utilizing PCR to obtain a partial cDNA sequence of the flightin protein. We then employed phylogenetic and sequence analysis to gain insights into this protein in flight-related adaptations. The cDNA has an 1189-base pair sequence including an open reading frame (453 bp) encoding 150 amino acids. Analyzing the deduced amino acid sequence using an online tool revealed a molecular weight of 18.05 kDa, an isoelectric point of 5.84, four functional site patterns, and no transmembrane topology. We constructed a phylogenetic tree of flightin based on 38 species. Our analysis indicated that V. basalis is most closely related to V. mandarinia; this alignment is consistent with their similar aggressive behavior, but their evolutionary relationship, based on mitochondrial sequences, presents a contrast. These initial findings on the flightin gene in V. basalis lay the groundwork for future functional studies to elucidate its specific role in flight adaptations and explore its potential as a target for pest management strategies.

Comparative Analysis of the Chloroplast Genomes of Eight Species of the Genus Lirianthe Spach with Its Generic Delimitation Implications.

Based on Sima and Lu's system of the family Magnoliaceae, the genus Lirianthe Spach s. l. includes approximately 25 species, each with exceptional landscaping and horticultural or medical worth. Many of these plants are considered rare and are protected due to their endangered status. The limited knowledge of species within this genus and the absence of research on its chloroplast genome have greatly impeded studies on the relationship between its evolution and systematics. In this study, the chloroplast genomes of eight species from the genus Lirianthe were sequenced and analyzed, and their phylogenetic relationships with other genera of the family Magnoliaceae were also elucidated. The results showed that the chloroplast genome sizes of the eight Lirianthe species ranged from 159,548 to 159,833 bp. The genomes consisted of a large single-copy region, a small single-copy region, and a pair of inverted repeat sequences. The GC content was very similar across species. Gene annotation revealed that the chloroplast genomes contained 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, totaling 130 genes. Codon usage analysis indicated that codon usage was highly conserved among the eight Lirianthe species. Repeat sequence analysis identified 42-49 microsatellite sequences, 16-18 tandem repeats, and 50 dispersed repeats, with microsatellite sequences being predominantly single-nucleotide repeats. DNA polymorphism analysis revealed 10 highly variable regions located in the large single-copy and small single-copy regions, among which rpl32-trnL, petA-psbJ, and trnH-psbA were the recommended candidate DNA barcodes for the genus Lirianthe species. The inverted repeat boundary regions show little variation between species and are generally conserved. The result of phylogenetic analysis confirmed that the genus Lirianthe s. l. is a monophyletic taxon and the most affinal to the genera, Talauma and Dugandiodendron, in Sima and Lu's system and revealed that the genus Lirianthe s. s. is paraphyletic and the genus Talauma s. l. polyphyletic in Xia's system, while Magnolia subsection Gwillimia is paraphyletic and subsection Blumiana polyphyletic in Figlar and Nooteboom's system. Morphological studies found noticeable differences between Lirianthe species in aspects including leaf indumentum, stipule scars, floral orientation, tepal number, tepal texture, and fruit dehiscence. In summary, this study elucidated the chloroplast genome evolution within Lirianthe and laid a foundation for further systematic and taxonomic research on this genus.

Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications.

Short tandem repeats (STRs) are a class of repetitive elements, composed of tandem arrays of 1-6 base pair sequence motifs, that comprise a substantial fraction of the human genome. STR expansions can cause a wide range of neurological and neuromuscular conditions, known as repeat expansion disorders, whose age of onset, severity, penetrance and/or clinical phenotype are influenced by the length of the repeats and their sequence composition. The presence of non-canonical motifs, depending on the type, frequency and position within the repeat tract, can alter clinical outcomes by modifying somatic and intergenerational repeat stability, gene expression and mutant transcript-mediated and/or protein-mediated toxicities. Here, we review the diverse structural conformations of repeat expansions, technological advances for the characterization of changes in sequence composition, their clinical correlations and the impact on disease mechanisms.

Vibrio misgurnus sp. nov., a new pathogen of cultured loach (Misgurnus anguillicaudatus), closely related to Vibrio cholerae

An epidemic with petechial hemorrhages on the body surface recently occurred in the farmed loach (Misgurnus anguillicaudatus) in Sichuan province. Multiple antibiotic treatments were ineffective against this epidemic. This study aims to elucidate the cause of the disease. Two bacterial strains, GVCT and VCS were isolated from diseased loach. Experimental infections with these two isolates resulted in marked symptoms in the loach consistent with those observed in natural outbreaks. The taxonomic status was determined by phenotypic assay, chemotaxonomic and whole genome analysis. Strain GVCT exhibited unique phenotypic characteristics, including its β-glucosidase activity and inability to utilize casein and starch, which distinguished it from Vibrio cholerae ATCC14035T. Paired 16S rRNA gene sequence analysis confirmed that strains GVCT and VCS belong to the genus Vibrio. The primary fatty acids of strain GVCT are C16:0, summed Feature 3 (C16:1ω7c/C16:1ω6c), and summed Feature 8 (C18:1 ω6c/C18:1 ω7c), and the major respiratory quinone is Q-8. The predominant lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), aminophospholipids (APL) and an unidentified phosphoglycolipid designated PL1. Strains GVCT and VCS have genome sizes of 3.2 Mb and 3.3 Mb, as well as GC contents of 47.0 and 47.2 mol% respectively. Phylogenomic and whole-genome nucleotide sequence analyses further confirmed that these isolates represent a novel species of the genus Vibrio, for which the name Vibrio misgurnus sp. nov. is proposed, with strain GVCT as the type strain. Strain GVCT was found to be highly pathogenic to loach, causing high mortality and posing a threat to loach aquaculture, with a half-lethal dose (LD50) of strain GVCT for loach is 8.96 × 106 CFU/mL, and it was resistant to drugs such as enrofloxacin, doxycycline hydrochloride, flumequine, neomycin sulphate and florfenicol.

An Integrated Approach Including CRISPR/Cas9-Mediated Nanopore Sequencing, Mate Pair Sequencing, and Cytogenomic Methods to Characterize Complex Structural Rearrangements in Acute Myeloid Leukemia.

Complex structural chromosome abnormalities such as chromoanagenesis have been reported in acute myeloid leukemia (AML). They are usually not well characterized by conventional genetic methods, and the characterization of chromoanagenesis structural abnormalities from short-read sequencing still presents challenges. Here, we characterized complex structural abnormalities involving chromosomes 2, 3, and 7 in an AML patient using an integrated approach including CRISPR/Cas9-mediated nanopore sequencing, mate pair sequencing (MPseq), and SNP microarray analysis along with cytogenetic methods. SNP microarray analysis revealed chromoanagenesis involving chromosomes 3 and 7, and a pseudotricentric chromosome 7 was revealed by cytogenetic methods. MPseq revealed 138 structural variants (SVs) as putative junctions of complex rearrangements involving chromosomes 2, 3, and 7, which led to 16 novel gene fusions and 33 truncated genes. Thirty CRISPR RNA (crRNA) sequences were designed to map 29 SVs, of which 27 (93.1%) were on-target based on CRISPR/Cas9 crRNA nanopore sequencing. In addition to simple SVs, complex SVs involving over two breakpoints were also revealed. Twenty-one SVs (77.8% of the on-target SVs) were also revealed by MPseq with shared SV breakpoints. Approximately three-quarters of breakpoints were located within genes, especially intronic regions, and one-quarter of breakpoints were intergenic. Alu and LINE repeat elements were frequent among breakpoints. Amplification of the chromosome 7 centromere was also detected by nanopore sequencing. Given the high amplification of the chromosome 7 centromere, extra chromosome 7 centromere sequences (tricentric), and more gains than losses of genomic material, chromoanasynthesis and chromothripsis may be responsible for forming this highly complex structural abnormality. We showed this combination approach's value in characterizing complex structural abnormalities for clinical and research applications. Characterization of these complex structural chromosome abnormalities not only will help understand the molecular mechanisms responsible for the process of chromoanagenesis, but also may identify specific molecular targets and their impact on therapy and overall survival.

Novel electroporation-based genome editing of carnation plant tissues using RNPs targeting the anthocyanidin synthase gene.

A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis. As the ANS of 'Kane Ainou 1-go' has not been previously isolated, we initially isolated the ANS gene from 'Kane Ainou 1-go' for characterization. Southern hybridization analysis confirmed that the ANS gene was present in the genome as a two-allele gene with a pair of homologous sequences (ANS-1 and 2); these sequences were used as the target for genome editing. Genome editing was performed by introducing #2_single-guide RNA into the stem tissue using the ribonucleoprotein. This molecule was used because it exhibited the highest efficiency in an analysis of cleavage activity against the target sequence in vitro. Cleaved amplified polymorphic sequence analysis of genomic DNA extracted from 85 regenerated individuals after genome editing was performed. The results indicated that mutations in the ANS gene may have been introduced into two lines. Cloning of the ANS gene in these two lines confirmed the introduction of a single nucleotide substitution mutation for ANS-1 in both lines, and a single amino acid substitution in one line. We discussed the possibility of color change by the amino acid substitution, and also the future applications of this technology.

Family Recall of and Response to Germline Pathologic Variants Found on Paired Tumor-Germline Sequencing in Pediatric Oncology.

Paired tumor-germline sequencing can identify somatic variants for targeted therapy and germline pathogenic variants (GPVs) causative of hereditary cancer/tumor predisposition syndromes. It is unknown how patients/families in pediatric oncology use information about an identified GPV. We assessed recall of germline results and actions taken on the basis of findings. We completed phone surveys with patients (and/or their parent) with GPVs identified via a single academic medical center's paired tumor-germline sequencing study. Seven hundred forty pediatric (aged 0-25 years) oncology patients were enrolled in this sequencing study between May 2012 and August 2021. Ninety-six participants (13.0%) had at least one GPV identified and were therefore eligible for this survey. The parent/guardian (for patients younger than 18 years or deceased patients) or patients themselves (if 18 years or older) were contacted. Survey topics included germline result recall, experience with genetic counseling, changes to patient's cancer treatment/screening, sharing of results with family members, and lifestyle changes. Fifty-three surveys (response rate, 55.2%) were completed between October 2021 and June 2022. Thirty-seven (69.8%) respondents correctly recalled the identified GPV. Discussing results with a genetic counselor (P = .0001), having a GPV related to the cancer/tumor diagnosis (P = .002), and non-Hispanic White race/ethnicity (P = .02) were associated with accurate recall. Twenty-five respondents (47.2%) reported a change in the child's cancer treatment and/or screening recommendations, 17 respondents (32.1%) made a lifestyle change on the basis of the results, and 44 respondents (83.0%) shared results with at least one family member. While most respondents remembered that a GPV was identified in the patient, some did not recall having a GPV found, and others recalled germline findings incorrectly. Future work may determine patient/family preferences for timing/method of result return to optimize patient recall and use of germline results.

Investigating the ability of deep learning-based structure prediction to extrapolate and/or enrich the set of antibody CDR canonical forms.

Deep learning models have been shown to accurately predict protein structure from sequence, allowing researchers to explore protein space from the structural viewpoint. In this paper we explore whether "novel" features, such as distinct loop conformations can arise from these predictions despite not being present in the training data. Here we have used ABodyBuilder2, a deep learning antibody structure predictor, to predict the structures of ~1.5M paired antibody sequences. We examined the predicted structures of the canonical CDR loops and found that most of these predictions fall into the already described CDR canonical form structural space. We also found a small number of "new" canonical clusters composed of heterogeneous sequences united by a common sequence motif and loop conformation. Analysis of these novel clusters showed their origins to be either shapes seen in the training data at very low frequency or shapes seen at high frequency but at a shorter sequence length. To evaluate explicitly the ability of ABodyBuilder2 to extrapolate, we retrained several models whilst withholding all antibody structures of a specific CDR loop length or canonical form. These "starved" models showed evidence of generalisation across CDRs of different lengths, but they did not extrapolate to loop conformations which were highly distinct from those present in the training data. However, the models were able to accurately predict a canonical form even if only a very small number of examples of that shape were in the training data. Our results suggest that deep learning protein structure prediction methods are unable to make completely out-of-domain predictions for CDR loops. However, in our analysis we also found that even minimal amounts of data of a structural shape allow the method to recover its original predictive abilities. We have made the ~1.5 M predicted structures used in this study available to download at https://doi.org/10.5281/zenodo.10280181.

Protein embedding based alignment

PurposeDespite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algorithms have been using substitution matrices since their creation in the 1970’s to generate alignments, however, these matrices do not work well to score alignments within the twilight zone. We developed Protein Embedding based Alignments, or PEbA, to better align sequences with low pairwise identity. Similar to the traditional Smith-Waterman algorithm, PEbA uses a dynamic programming algorithm but the matching score of amino acids is based on the similarity of their embeddings from a protein language model.MethodsWe tested PEbA on over twelve thousand benchmark pairwise alignments from BAliBASE, each one extracted from one of their multiple sequence alignments. Five different BAliBASE references were used, each with different sequence identities, motifs, and lengths, allowing PEbA to showcase how well it aligns under different circumstances.ResultsPEbA greatly outperformed BLOSUM substitution matrix-based pairwise alignments, achieving different levels of improvements of the alignment quality for pairs of sequences with different levels of similarity (over four times as well for pairs of sequences with <10% identity). We also compared PEbA with embeddings generated by different protein language models (ProtT5 and ESM-2) and found that ProtT5-XL-U50 produced the most useful embeddings for aligning protein sequences. PEbA also outperformed DEDAL and vcMSA, two recently developed protein language model embedding-based alignment methods.ConclusionOur results suggested that general purpose protein language models provide useful contextual information for generating more accurate protein alignments than typically used methods.

ANALYSIS OF THE CRYPTOSPORIDIUM SPP GP60 GENE VARIABILITY APPLYING INFORMATION THEORY

In this paper we used statistical methods to understand the genetic information of DNA considered as a statistical system. The alphabet of a DNA sequence is defined by the four nucleotides: adenine, cytosine, guanine, and thymine. The order of nucleotides along the DNA sequences encodes the genetic information. We have analyzed three Cryptosporidium DNA sequences: one DNA sequence isolated and analyzed in our laboratory and two DNA reference sequences from the public database GenBank. Each DNA sequence is considered as a statistical system and is represented by a random variable and an associate probability distribution. The Shannon entropy, Renyi entropy, Onicescu informational energy and square deviation from uniform distribution are used in order to measure the degree of randomness for the three statistical systems. The similarity and difference between the three DNA sequences of the two Cryptosporidium species (Cryptosporidium hominis and Cryptosporidium parvum) were assessed by calculating the statistical distance between the probability distributions associated with each pair of DNA sequences. Each of the three DNA sequences pairs with one of the other two sequences and forms three pairs of sequences. Using the associated probability distributions, the statistical distance between them can be calculated. Bhattacharyya distance measures similarity degree between the two probability distributions. The Kullback-Leiber and the resistor-average distances measure the difference between the two distributions.

A NEW SPECIES OF THELOHANELLUS (CNIDARIA: MYXOSPOREA: MYXOBOLIDAE) FROM THE GILL OF QUILLBACK, CARPIODES CYPRINUS (CYPRINIFORMES: CATOSTOMIDAE), FROM THE ARKANSAS RIVER DRAINAGE OF OKLAHOMA.

During May 2022 and again in March 2023, 5 quillbacks, Carpiodes cyprinus, were collected from the Verdigris River, Wagoner County, Oklahoma (n = 1), and the Black River, Lawrence County, Arkansas (n = 4), and their gill, gallbladder, fins, integument, musculature, and other major organs were macroscopically examined for myxozoans. Gill lamellae from the single quillback from the Verdigris River was infected with a new myxozoan, Thelohanellus oklahomaensis n. sp. Qualitative and quantitative morphological data were obtained from fresh and formalin-fixed preserved myxospores, and molecular data consisted of a 1,767 base pair sequence of the partial small subunit (SSU) ribosomal RNA gene. Phylogenetic analysis grouped T. oklahomaensis n. sp. with myxozoans known to infect North American catostomids and Eurasian cyprinids. Histological examination localized plasmodia to an intralamellar developmental site and revealed a possible vestige of a second polar capsule. Although plasmodia markedly expanded lamellae, there were no associated epithelial or inflammatory changes. Thelohanellus oklahomaensis n. sp. is the only member of the genus known to infect the gills of C. cyprinus.

Primer Design and in Silico PCR for Detection Microsatellite Locus on Cassava (Manihot esculenta) as an Early Study of Genetic Diversity of Gluten Free Food Crops

Food allergy is a hypersensitive reaction of the body to certain substances that should not be harmful. One of the basic ingredients of foods that are reported to contain allergens is wheat. The type of allergen in wheat is found in gluten, which produces the protein gliadin. The protein gliadin is thought to be the cause of allergic reactions, especially in children and people who have celiac disease. Local food ingredients such as cassava can be used as alternative raw materials for gluten-free food products. The genetic diversity test of cassava is needed to determine the genetic variation of the cassava population and the ability to adapt to natural surroundings. Study of genetic diversity of a plant population can be analyzed by DNA fingerprinting technique using microsatellite molecular markers in the PCR method. Primer selection is a crucial stage because the position of the primer attachment will determine the success of the amplification process. Primer design and in silico PCR assay were carried out as a preliminary study to design the right primer to attach to a specific template. The method used digitally with the help of the NCBI Pick Primer page and FastPCR software for PCR stimulation, knowing the position of the primer attachment, precisely determining the primer and the length of the resulting amplicon. The results obtained in the form of 5 pairs of primer sequences attached to the microsatellite polymorphic locus. The length of the amplicon produced in each primer was 167 bp, 195 bp, 155 bp, 161 bp and 112 bp. The basis of primer selection consists of the length of the primary base, the TM value (melting temperature), the percentage of GC amount and the possibility of the formation of dimers between primers.