High-throughput Sequencing Assay Research Articles

Multiscale Poisson process approaches for detecting and estimating differences from high-throughput sequencing assays

Multiscale Poisson process approaches for detecting and estimating differences from high-throughput sequencing assays

Protocell Effects on RNA Folding, Function, and Evolution.

ConspectusCreating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles.The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RNA. Because of the exponential dynamics of replication and selection, even small changes to activity and function could lead to major evolutionary consequences. By closely studying the details of minimal yet surprisingly complex protocells, we might one day trace a pathway from encapsulated RNA to a living system.

Role of LsrR in the regulation of biofilm formation in mammary pathogenic Escherichia coli

BackgroundMammary Pathogenic Escherichia coli (MPEC) is an important pathogen that can escape the attack of the host immune system through biofilm formation and proliferate in the mammary gland continuously, resulting in mastitis in cows and causing enormous economic losses. As an effector of AI-2 quorum sensing, LsrR extensively affects the expression levels of hundreds of genes related to multiple biological processes in model E. coli strain. However, the regulatory role of LsrR in MPEC and whether it is involved in pathogenesis has been seldom reported.ResultsIn this study, the function of LsrR in strain MPEC5, obtained from a milk sample in dairy cows with mastitis, was investigated by performing high-throughput sequencing (RNA-seq) assays. The results revealed that LsrR down-regulated the transcript levels of fimAICDFGH (encoding Type 1 pili), which have been reported to be associated with biofilm formation process. Biofilm assays confirmed that deletion of lsrR resulted in a significant increase in biofilm formation in vitro. In addition, electrophoretic mobility shift assay (EMSA) provided evidence that LsrR protein could directly bind to the promoter regions of fimAICDFGH in a dose-dependent manner.ConclusionsThese results indicate that LsrR protein inhibits the biofilm formation ability of MPEC5 by directly binding to the fimAICDFGH promoter region. This study presents a novel clue for further exploration of the prevention and treatment of MPEC.

Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India

BackgroundCurrent clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India.Results903 smMIPs were designed to target exon and exon–intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood.ConclusionWe developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Preconditioning Exercise Inhibits Neuron Ferroptosis and Ameliorates Brain Ischemia Damage by Skeletal Muscle-Derived Exosomes via Regulating miR-484/ACSL4 Axis.

Aims: Although there is evidence that patients with stroke who exercise regularly before stroke have a better prognosis than those who do not exercise, the detailed mechanism remains unclear. Moreover, neuronal death plays a central role in neurological dysfunction caused by ischemic stroke. Thus, we investigated whether exercise could reduce stroke-induced neuronal death and its associated mediators in the current study. Results: Ferroptosis was the most dominant form of programmed cell death in neurons. Preconditioning exercise before stroke improved the neurological function and decreased the infarct area in rats with ischemic stroke. Preconditioning exercise attenuated stroke-induced ferroptosis by reducing lipid peroxidation (LPO) production, upregulating glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11 (SLC7A11), and downregulating acyl-CoA synthetase long-chain family member 4 (ACSL4). High-throughput sequencing and dual luciferase reporter assays revealed that exercise-induced exosomal miR-484 inhibits Acsl4 expression. Moreover, we showed that exercise-induced exosomal miR-484 is mainly derived from skeletal muscle, and the neuroprotective effect of preconditioning exercise is suppressed by inhibiting miR-484 production in skeletal muscle. Innovation: This study suggested that neuronal ferroptosis is the most dominant form of programmed cell death in a hypoxic environment. Moreover, we showed that the ferroptosis pathway is a potential therapeutic target in ischemic stroke and that preconditioning exercise could be an effective antioxidant intervention for cerebral ischemia. Conclusion: Our work revealed that preconditioning exercise before stroke exerts neuroprotective effects against brain ischemia by skeletal muscle-derived exosomal miR-484 via inhibiting ferroptosis.

Blocking cGAS-STING pathway promotes post-stroke functional recovery in an extended treatment window via facilitating remyelination

Ischemic stroke is a major cause of worldwide death and disability, with recombinant tissue plasminogen activator being the sole effective treatment, albeit with a limited treatment window. The cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) pathway is emerging as the major DNA-sensing pathway to invoke immune responses in neuroinflammatory disorders. By performing a series of neurobehavioral assessments, electrophysiological analysis, high-throughput sequencing, and cell-based assays based on the transient middle cerebral artery occlusion (tMCAO) mouse stroke model, we examined the effects and underlying mechanisms of genetic and pharmacological inhibition of the cGAS-STING pathway on long-term post-stroke neurological functional outcomes. Blocking the cGAS-STING pathway, even 3days after tMCAO, significantly promoted functional recovery in terms of white matter structural and functional integrity as well as sensorimotor and cognitive functions. Mechanistically, the neuroprotective effects via inhibiting the cGAS-STING pathway were contributed not only by inflammation repression at the early stage of tMCAO but also by modifying the cell state of phagocytes to facilitate remyelination at the sub-acute phase. The activation of the cGAS-STING pathway significantly impeded post-stroke remyelination through restraining myelin debris uptake and degradation and hindering oligodendrocyte differentiation and maturation. Manipulating the cGAS-STING pathway has an extended treatment window in promoting long-term post-stroke functional recovery via facilitating remyelination in a mouse stroke model. Our results highlight the roles of the cGAS-STING pathway in aggregating stroke pathology and propose a new way for improving functional recovery after ischemic stroke. This work was primarily funded by the National Key R&D Program of China.

Exploring the key deteriorative microorganisms on ancient ivories unearthed from the Sanxingdui Ruins site during temporary cold storage.

The ancient ivories unearthed from the Sanxingdui Ruins site are valuable cultural relics, however, the microbial biodeterioration on ivories during temporary cold storage poses a great threat to their later long-term preservation. Here, the combination of high-throughput sequencing and biochemical assays was applied for the in-depth investigation of the key deteriorative microorganisms colonizing on the ivories and the tracing of their origin, as well as the assessment of the ethanol disinfection impact on the microbial communities on ivories. It was observed that the surfaces of ivories were scattered by the fungal patches of white, dark grey, and hedge green colors during cold storage. The high-throughput sequencing results showed that the genera Mortierella (38.51%), Ilyonectria (14.43%), Penicillium (1.15%), and Aspergillus (1.09%) were the dominant fungi, while Pseudomonas (22.63%), Sphingopyxis (3.06%), and Perlucidibaca (2.92%) were the dominant bacteria on ivories. The isolated Aspergillus A-2 resulted in the highest amount of calcium releasing from the degradation of hydroxyapatite (HAP), the main component of ivory, by the organic acids produced, including oxalic acid and citric acid. The fast expectation-maximization for microbial source tracking (FEAST) analysis revealed that the majority of the fungi (57.45%) and bacteria (71.84%) colonizing on the ivories were derived from the soils surrounding ivories in the sacrifice pits, indicating soils as the primary source for the spoilage microbes growing on ivories. The dominant strains could degrade cellulose, the key components of wet cotton towels commonly applied on ivories for moisture maintenance, aiding the spoilage microbes colonizing on ivories. Notably, the ivory disinfection with 75% ethanol during the cleansing significantly decreased the relative abundance of the dominant genera of Ilyonectria, Aspergillus, and Pseudomonas, with Mortierella becoming the dominant one on ivories. Together, the fungi, particularly Aspergillus and Penicillium, played a significant role in the microbial biodeterioration of unearthed ancient ivories by producing the organic acids. These results may improve the control of the microbial biodeterioration and develop more efficient strategies for the long-time conservation of unearthed ancient ivories and other cultural relics.

Robust and sensitive amplicon-based whole-genome sequencing assay of respiratory syncytial virus subtype A and B.

In this paper, we report an improved high-throughput respiratory syncytial virus (RSV) whole-genome sequencing (WGS) assay performed directly on clinical samples, using a 4-primer-pool, short-amplicon PCR-tiling approach that is suitable for short-read sequencing platforms. The RSV WGS approach described in this study has increased sensitivity compared to previous approaches and can be applied to clinical specimens without the requirement for enrichment. The updated approach produces sequences of high quality consistently and cost-effectively, suitable for implementation to underpin national and global programs for the surveillance of RSV genomic variation. The quality of sequence produced is essential for preparedness for new interventions in monitoring antigenic escape, where a single point mutation might lead to a reduction in antibody binding effectiveness and neutralizing activity, or indeed in the monitoring of retaining susceptibility to neutralization by existing and new interventions.

Single-cell transcriptome atlas reveals somatic cell embryogenic differentiation features during regeneration.

Understanding somatic cell totipotency remains a challenge facing scientific inquiry today. Plants display remarkable cell totipotency expression, illustrated by single-cell differentiation during somatic embryogenesis (SE) for plant regeneration. Determining cell identity and exploring gene regulation in such complex heterogeneous somatic cell differentiation have been major challenges. Here, we performed high-throughput single-cell sequencing assays to define the precise cellular landscape and revealed the modulation mode of marker genes during embryogenic differentiation in cotton (Gossypium hirsutum L.) as the crop for biotechnology application. We demonstrated that nonembryogenic calli (NEC) and primary embryogenic calli (PEC) tissues were composed of heterogeneous cells that could be partitioned into four broad populations with six distinct cell clusters. Enriched cell clusters and cell states were identified in NEC and PEC samples, respectively. Moreover, a broad repertoire of new cluster-specific genes and associated expression modules were identified. The energy metabolism, signal transduction, environmental adaptation, membrane transport pathways, and a series of transcription factors were preferentially enriched in cell embryogenic totipotency expression. Notably, the SE-ASSOCIATED LIPID TRANSFER PROTEIN (SELTP) gene dose-dependently marked cell types with distinct embryogenic states and exhibited a parabolic curve pattern along the somatic cell embryogenic differentiation trajectory, suggesting that SELTP could serve as a favorable quantitative cellular marker for detecting embryogenic expression at the single-cell level. In addition, RNA velocity and Scissor analysis confirmed the pseudo-temporal model and validated the accuracy of the scRNA-seq data, respectively. This work provides valuable marker-genes resources and defines precise cellular taxonomy and trajectory atlases for somatic cell embryogenic differentiation in plant regeneration.

Tumor-derived small extracellular vesicles facilitate omental metastasis of ovarian cancer by triggering activation of mesenchymal stem cells

BackgroundOmental metastasis is the major cause of ovarian cancer recurrence and shortens patient survival, which can be largely attributed to the dynamic evolution of the fertile metastatic microenvironment driven by cancer cells. Previously, we found that adipose-derived mesenchymal stem cells (ADSCs) undergoing a phenotype shift toward cancer-associated fibroblasts (CAFs) participated in the orchestrated omental premetastatic niche for ovarian cancer. Here, we aim to elucidate the underlying mechanisms.MethodsSmall extracellular vesicles were isolated from ovarian cancer cell lines (ES-2 and its highly metastatic subline, ES-2-HM) and patient ascites using ultracentrifugation. Functional experiments, including Transwell and EdU assays, and molecular detection, including Western blot, immunofluorescence, and RT–qPCR, were performed to investigate the activation of ADSCs in vitro. High-throughput transcriptional sequencing and functional assays were employed to identify the crucial functional molecules inducing CAF-like activation of ADSCs and the downstream effector of miR-320a. The impact of extracellular vesicles and miR-320a-activated ADSCs on tumor growth and metastasis was assessed in subcutaneous and orthotopic ovarian cancer xenograft mouse models. The expression of miR-320a in human samples was evaluated using in situ hybridization staining.ResultsPrimary human ADSCs cocultured with small extracellular vesicles, especially those derived from ES-2-HM, exhibited boosted migration, invasion, and proliferation capacities and elevated α-SMA and FAP levels. Tumor-derived small extracellular vesicles increased α-SMA-positive stromal cells, fostered omental metastasis, and shortened the survival of mice harboring orthotopic ovarian cancer xenografts. miR-320a was abundant in highly metastatic cell-derived extracellular vesicles, evoked dramatic CAF-like transition of ADSCs, targeted the 3′-untranslated region of integrin subunit alpha 7 and attenuated its expression. miR-320a overexpression in ovarian cancer was associated with omental metastasis and shorter survival. miR-320a-activated ADSCs facilitated tumor cell growth and omental metastasis. Depletion of integrin alpha 7 triggered CAF-like activation of ADSCs in vitro.8TP37CR9mn1qNp5Xi3wswYVideo ConclusionsmiR-320a in small extracellular vesicles secreted by tumor cells targets integrin subunit alpha 7 in ADSCs and drives CAF-like activation, which in turn facilitates omental metastasis of ovarian cancer.Graphical

Effects of stroke on the intestinal biota in diabetic mice and type 2 diabetic patient biota.

The intestinal biota, known for its colonization of the human intestine and its modulation of host pathophysiological responses through the immune and endocrine systems, has gained substantial interest in recent years due to its notable correlation with diabetes and stroke. In order to examine this association, a comparative study was conducted on the intestinal biota and blood samples obtained from mouse models and type 2 diabetic patients with and without stroke complications. Advanced techniques, such as high-throughput sequencing and enzyme-linked immunosorbent assay were employed to identify the differences in the intestinal biota and blood indices of mouse models and patients. At the phylum level, the dominant gut bacteria identified in patients with diabetes mellitus and stroke were Firmicutes, Bacteroidetes, and Proteobacteria. It was noteworthy that the relative abundance of Bacteroides at the genus level was significantly diminished in the DB-PT group (photothrombotic diabetes mice) as compared to the DB group (diabetesmice). This result was consistent with observations in human samples. Additionally, significant variations were detected in lipid proteins, specifically APOA4, in diabetic patients with and without stroke. Stroke can diminish the abundance and diversity of intestinal biota, potentially correlating with lipid proteins in patients with diabetes.

Tumor-Infiltrating Normal B Lymphocytes Have Remarkable Prognostic Effects and Are Crucial for Antitumor Immune Responses in Diffuse Large B-Cell Lymphoma

Introduction: In recent years, increasing evidence suggests an important role of tumor-infiltrating B lymphocytes (TIL-Bs) in cancer immunity. In various types of solid tumors, high density of TIL-Bs and presence of mature tertiary lymphoid structures consistently correlate with better prognosis and response to immune checkpoint blockade therapies. Diffuse large B-cell lymphoma (DLBCL) is a type of aggressive lymphoma arising from mature B cells. TIL-Bs have been identified in DLBCL based on single-cell gene-expression data in several previous studies, but their prognostic significance in DLBCL is unknown. In this study, we determined the clinical significance of TIL-B abundance and investigated the potential underlying mechanisms. Patients and Methods: This abstract includes a discovery study in which we distinguished TIL-Bs from malignant B-cells by immunoglobulin gene (IG) clonotype analysis and a validation study using flow cytometry. In the discovery study, a molecularly well-characterized DLBCL cohort assembled by the International DLBCL R-CHOP Consortium Program was analyzed. DNA samples from DLBCL patients were sequenced by high-throughput ultra-deep sequencing assays using multiplexed forward and reverse primers. Based on the IG heavy chain (IGH) sequencing results, malignant B-cell and TIL-B VDJ clonotypes were identified for 138 patients, and the frequencies and numbers of TIL-B clonotypes in individual sequence repertoires were calculated. In 79 DLBCL cases, a DJ-only sequence was predominant and no productive VDJ sequences met the criteria for diagnostic sequences. Total frequencies of productive VDJ sequences in the sequence repertoires were then used to access high and low TIL-B frequencies. TIL-B frequencies were also evaluated by IG light chain clonotypes for these 217 patients and additional 52 patients. The TIL-B frequencies were correlated with patient survival, gene-expression profiling (GEP) data GSE31312, and frequencies of DLBCL-infiltrating immune cells quantified by fluorescent multiplex immunohistochemistry (mIHC). To validate the prognostic significance of TIL-B frequencies, we assembled a validation cohort of 94 DLBCL patients treated at Duke University Medical Center. TIL-Bs in tissues were quantified by flow cytometry immunophenotyping. Ratios of TIL-Bs to abnormal B cells were assessed for prognostic effects. Results: First, we found thathigh frequencies of TIL-Bs and clonotypic diversity were associated with significantly favorable prognostic effects in 138 DLBCL patients with their malignant B-cell IGH-VDJ clonotypes identified (Figure A). The prognostic effects of TIL-Bs outweighed those of the germinal center B-cell-like/activated B-cell-like classification (Figure B). Second, patients with high frequencies of TIL-Bs compared with those without had significant upregulation of immune response genes by GEP (Figure C), higher CD4 T cell infiltration quantified by fluorescent mIHC (Figure D), and enrichment of EcoTyper-defined specific cell states, including significantly increased frequencies of B cell state S2 (pre-memory), CD4 T cell state S3 (naïve), follicular helper T cell state S3, and endothelial cell state S3, whereas lower frequencies of B cell state S5 (plasmablast) and follicular helper T cell state S1. Third, high TIL-B abundance in 79 ‘DJ-only’ clonotype cases and additional 52 cases assessed by light chain clonotype analysis showed similar favorable prognostic effects and associations with upregulated immune gene expression and CD4 T cell infiltration. Fourth, the identified GEP signatures, prominent with genes involved in T-dependent B cell activation and T cell activation and differentiation, showed significant prognostic effects in two GEO datasets. Fifth, TIL-B abundance showed significant prognostic effects in DLBCL cases infiltrated with T-cells in both the discovery study (Figure E) and validation study (Figure F, flow cytometry cohort). Conclusions: TIL-B frequencies and clonotypic diversity have remarkable prognostic and biological effects in DLBCL, which has significant implications for developing novel therapeutic strategies. Our study identified a new prognostic biomarker in DLBCL and an important player in anti-lymphoma immune responses, providing a new point of view to analyze the tumor biology in aggressive B-cell lymphoma and precisely identify prognostic determinants.

Combined Multiplexed Phage Display, High-Throughput Sequencing, and Functional Assays as a Platform for Identifying Modulatory VHHs Targeting the FSHR.

Developing modulatory antibodies against G protein-coupled receptors is challenging. In this study, we targeted the follicle-stimulating hormone receptor (FSHR), a significant regulator of reproduction, with variable domains of heavy chain-only antibodies (VHHs). We built two immune VHH libraries and submitted them to multiplexed phage display approaches. We used next-generation sequencing to identify 34 clusters of specifically enriched sequences that were functionally assessed in a primary screen based on a cAMP response element (CRE)-dependent reporter gene assay. In this assay, 23 VHHs displayed negative or positive modulation of FSH-induced responses, suggesting a high success rate of the multiplexed strategy. We then focused on the largest cluster identified (i.e., PRC1) that displayed positive modulation of FSH action. We demonstrated that PRC1 specifically binds to the human FSHR and human FSHR/FSH complex while potentiating FSH-induced cAMP production and Gs recruitment. We conclude that the improved selection strategy reported here is effective for rapidly identifying functionally active VHHs and could be adapted to target other challenging membrane receptors. This study also led to the identification of PRC1, the first potential positive modulator VHH reported for the human FSHR.

Monitoring of Systemic Light-Chain Amyloidosis Patients Using Mass Spectrometry (M-inSight) in Serum

Introduction: Systemic light-chain amyloidosis (AL) is a rare disorder characterized by extracellular deposition of monoclonal light-chain immunoglobulins forming insoluble aggregates in different organs. Kidney, heart and liver are principal organs affected by the disease inducing dysfunctions and failures. In this disease, even a low level of circulating light chain can cause significant damages, making challenging the measure of disease burden via peripheral blood. Although a bone marrow aspiration is required to confirm the diagnosis, the evolution of the disease is usually monitored using free light chains dosage, serum and urine electrophoresis, as well as immunofixation. However, these techniques have demonstrated some limitations in terms of sensitivity. Sebia had recently introduced M-inSight TM, a novel, ultra-sensitive and non-invasive assay for monitoring low level disease on blood using targeted mass spectrometry. In this pilot study, M-inSight TM technology is employed to assess the use of mass spectrometry to monitor AL patients. Methods: 14 AL patients were selected to assess the use of M-InSight to detect and quantify AL light chain. 8/14 patients were selected from the AMYDARA study (NCT02816476), consisting in refractory patients treated with Daratumumab. Serum free light-chain assay (Freelite TM), immunofixation on serum/urine as well as bone marrow collection for DNA (ClonoSeq) and RNA (RACE-RepSeq) immunoglobulin next generation sequencing were used to monitor the disease at baseline and end of treatment (EOT) and compared to M-inSight TM. Additionally, 6/14 multicenter patients with normal free light chain level at diagnosis were selected to evaluate the sensitivity of M-InSight. Total mRNA was extracted from BM samples, retrotranscribed to cDNA and then used for immunoglobulin repertoire high-throughput sequencing assay (RACE-RepSeq). cDNA assembly pipeline using IMGT/HighV-QUEST and Vidjil software were used to construct clonotypes and to identify clonal molecular fingerprints and finally their clonotypic peptides for M-InSight analysis. This technology consists of sequence the AL light chain from serum sample and choose clonotypic peptides from the hypervariable regions which then tracked down in the follow-up sample. Results Clonotypic peptides were identified in all eight patients from the baseline sample, which were then confirmed by mass spectrometry. Out of the 8 AMYDARA patients, 5/8 patients achieved very good partial response (VGPR), 2/8 achieved partial response (PR) and 1/8 resulted in complete response (CR). 6 patients had a decrease of the dFLC ratio measure with Freelite TM of 80% or more. 6 out of these 8 patients had MS data highly concordant with that of the serum free light-chain assay. 2 patients had a strong decrease in dFLC while MS measurements were stable or increased. However, detection of the clonotype using RACE-RepSeqand Clonoseq remained elevated, which was more in line with MS than Freelite TM. All patients with normalization of their dFLC were still detected using M-inSight, even those reaching MRD negativity (1 patient) or low number of cells (~10-5, 2 patients) by ClonoSeq. These results were consistent with the RACE-RepSeq which detected the light chain clonotypes in all patients at EOT. Clonotypic peptides using M-InSight were also detected in all 7 patients with normal free light chain at diagnosis. However, in one bi-clonal patient, peptides from only one of both chains were detected, suggesting that only one clone was secreting light chain. Conclusion The goal of this study was to evaluate the M-InSight technique to monitor the evolution of systemic AL amyloidosis in blood samples. The results showed a high concordance with bone marrow MRD measurement and a higher sensitivity than dFLC to monitor the disease. This study shows that MRD monitoring on blood is feasible, using an ultra-sensitive MS technique, avoiding invasive bone-marrow aspirate. M-inSight can track low level AL disease.

Ythdf2-mediated STK11 mRNA decay supports myogenesis by inhibiting the AMPK/mTOR pathway

An emerging research focus is the role of m6A modifications in mediating the post-transcriptional regulation of mRNA during mammalian development. Recent evidence suggests that m6A methyltransferases and demethylases play critical roles in skeletal muscle development. Ythdf2 is a m6A “reader” protein that mediates mRNA degradation in an m6A-dependent manner. However, the specific function of Ythdf2 in skeletal muscle development and the underlying mechanisms remain unclear. Here, we observed that Ythdf2 expression was significantly upregulated during myogenic differentiation, whereas Ythdf2 knockdown markedly inhibited myoblast proliferation and differentiation. Combined analysis of high-throughput sequencing, Co-IP, and RIP assay revealed that Ythdf2 could bind to m6A sites in STK11 mRNA and form an Ago2 silencing complex to promote its degradation, thereby regulating its expression and consequently, the AMPK/mTOR pathway. Furthermore, STK11 downregulation partially rescued Ythdf2 knockdown-induced impairment of proliferation and myogenic differentiation by inhibiting the AMPK/mTOR pathway. Collectively, our results indicate that Ythdf2 mediates the decay of STK11 mRNA, an AMPK activator, in an Ago2 system-dependent manner, thereby driving skeletal myogenesis by suppressing the AMPK/mTOR pathway. These findings further enhance our understanding of the molecular mechanisms underlying RNA methylation in the regulation of myogenesis and provide valuable insights for conducting in-depth studies on myogenesis.

Characterization of chromatin accessibility and gene expression reveal the key genes involved in cotton fiber elongation.

Cotton (Gossypium hirsutum L.) is an important economic crop, and cotton fiber is one of the longest plant cells, which provides an ideal model for the study of cell elongation and secondary cell wall synthesis. Cotton fiber length is regulated by a variety of transcription factors (TF) and their target genes; however, the mechanism of fiber elongation mediated by transcriptional regulatory networks is still unclear to a large extent. Here, we used a comparative assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) assay and RNA-seq analysis to identify fiber elongation transcription factors and genes using the short-fiber mutant ligon linless-2 (Li2 ) and wild type (WT). A total of 499 differential target genes were identified and GO analysis shows that differential genes are mainly involved in plant secondary wall synthesis and microtubule-binding processes. Analysis of the genomic regions preferentially accessible (Peak) has identified a number of overrepresented TF-binding motifs, highlighting sets of TFs that are important for cotton fiber development. Using ATAC-seq and RNA-seq data, we have constructed a functional regulatory network of each TF regulatory target gene and also the network pattern of TF regulating differential target genes. Further, to obtain the genes related to fiber length, the differential target genes were combined with FLGWAS data to identify the genes highly related to fiber length. Our work provides new insights into cotton fiber elongation.

Core autotrophic microbes drive functional stability of soil cbbL-containing autotrophic microbes during desertification

The desertification process is characterized by the degradation of soil habitats and attenuation of plant biomass, leading to decreased soil carbon (C) input and increased environmental stress gradients of soil microbes. C dioxide assimilation driven through autotrophic microorganisms is the main process of soil C cycling, and the ecological role of autotrophic microbes is critical for soil C sequestration. However, the feedback dynamics of autotrophic microbes and their functional activity in soil profiles during desertification have not been explored. Here, we analysed three typical stages of desertification (potential, moderate and severe desertification) by high-throughput sequencing and enzyme activity assays to investigate the variation trends of autotrophic microbes and the maintenance of C fixation activity along soil profiles (0–100 cm) as desertification proceeded. We found that the desertification process reduced the abundance and diversity of autotrophic microbes, but increased the activity of soil microbial C fixation enzymes, which highlights the importance of microbial CO2 fixation in oligotrophic soil profiles in desert ecosystems. In particular, we demonstrated that core autotrophic microbes drove the compositional difference of autotrophic microbes, which in turn affected soil C fixation activity, suggesting that core autotrophic microbes are critical for maintaining C sequestration during desertification. Taken together, these results strengthen our comprehension of the factors driving soil functional stability and emphasize that core microbes should be viewed as pivotal factors in maintaining functional activity and ecosystem sustainability during desertification.

17th International Conference on Malignant Lymphoma, Palazzo dei Congressi, Lugano, Switzerland, 13 - 17 June, 2023.

Introduction: ALK-positive anaplastic large cell lymphomas (ALCL) are characterized by rearrangements involving the ALK gene on chromosome 2. The translocation t(2;5) (p23;q35) resulting in the NPM1::ALK gene fusion is detected in the majority of ALCL. In 10%–20% of ALCL, ALK is fused to various other partner genes. Compared to NPM1::ALK, variant ALK-fusion proteins are not expressed in the nucleus. The frequency, distribution, and possible prognostic significance of the different variant ALK partner genes have not been analyzed in population-based studies so far. We investigated all patients with ALK-positive ALCL with exclusive cytoplasmic ALK-expression diagnosed in a uniformly treated cohort of ALCL patients in the NHL-BFM study group. Patients and Methods: Between 2000 and 2017, 312 children and adolescents were diagnosed with an ALK-positive ALCL in Austria, Germany, Switzerland and the Czech Republic, and included in the ALCL 99 trial or the NHL-BFM registry 2012. Reference pathology demonstrated exclusive cytoplasmic ALK-staining in 49 tumors. Formalin-fixed-paraffin-embedded or frozen tumors of 43/49 patients were available for molecular analyses. Tumor-DNA was analyzed by an ALK-specific genomic capture high throughput sequencing assay. ALK-partner gene-specific RT-PCR assays were used to identify the respective partner genes when tumor cDNA was available. Results: 41 of 43 available tumors with exclusive cytoplasmic ALK-staining could be analyzed. 13 were NPM1::ALK positive and 28 tumors had a variant ALK partner. TPM3::ALK (n = 9, 32%) and ATIC::ALK (n = 8, 29%) were the most common variant partner genes. XPOI could be identified as a novel ALK fusion partner. The patients´ characteristics of ALCL expressing Variant::ALK were comparable to those with NPM1::ALK fusions. The five-year event-free survival (EFS) and overall survival were comparable between the 284 NPM1::ALK and the group of 28 different Variant::ALK-expressing patients. However, none of the 9 patients with TPM3::ALK positive ALCL relapsed, compared to 5 relapses among 8 patients with ATIC::ALK positive ALCL. Conclusions: In our population-based cohort of ALK-positive ALCL-patients, less than 10% carried variant ALK-fusion partners, 60% of which were TPM3 or ATIC. In patients with exclusive cytoplasmic ALK staining patterns, NPM1::ALK positivity should be excluded by molecular analysis. The tendency of a different relapse risk between ATIC::ALK and TPM3::ALK -positive ALCL-patients suggests that the fusion partner might confer tumor aggressiveness or drug resistance. The research was funded by: KNACK DEN KREBS Fördergemeinschaft Kinderkrebs-Zentrum Hamburg e.V. and HAMBURGER STIFTUNG ZUR FÖRDERUNG DER KREBSBEKÄMPFUNG Keyword: diagnostic and prognostic biomarkers No conflicts of interests pertinent to the abstract.

TGF-β-p-STAT1-LAIR2 axis has a "self-rescue" role for exhausted CD8+ T cells in hepatocellular carcinoma.

TGF-β is related to the function of T cells in the tumor microenvironment. However, the characteristics of TGF-β affecting the function of CD8+ T cells in hepatocellular carcinoma (HCC) have not been clearly resolved. In this study, flow cytometry, mass cytometry, immunohistochemistry, RNA-seq, single-cell RNA-seq, assay for transposase-accessible chromatin with high throughput sequencing, chromatin immunoprecipitation, and dual-luciferase reporter gene assay were used to study the regulatory effect and molecular mechanism of TGF-β on HCC infiltrating CD8+ T cells. Here, we demonstrated that the overall effect of TGF-β on CD8+ T cells in HCC was to activate p-p38 to induce exhaustion, but it also initiated cell-intrinsic resistance mechanisms: 1) TGF-β upregulated the levels of p-STAT1 (S727) and promoted LAIR2 secretion; 2) the TGF-β-p-STAT1-LAIR2 axis relieved CD8+ T cells from exhaustion, which we called "self-rescue"; 3) this "self-rescue" behavior showed time and dose limitations on TGF-β stimulation, which was easily masked by stronger inhibitory signals; 4) the function of CD8+ T cells was improved by using TAK-981 to amplify "self-rescue" signal. Our study describes a "self-rescue" mechanism of CD8+ T cells in HCC against exhaustion and the good effects from amplifying this signal.

Insights into IGH clonal evolution in BCP-ALL: frequency, mechanisms, associations, and diagnostic implications.

The malignant transformation leading to a maturation arrest in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) occurs early in B-cell development, in a pro-B or pre-B cell, when somatic recombination of variable (V), diversity (D), and joining (J) segment immunoglobulin (IG) genes and the B-cell rescue mechanism of VH replacement might be ongoing or fully active, driving clonal evolution. In this study of newly diagnosed BCP-ALL, we sought to understand the mechanistic details of oligoclonal composition of the leukemia at diagnosis, clonal evolution during follow-up, and clonal distribution in different hematopoietic compartments. Utilizing high-throughput sequencing assays and bespoke bioinformatics we identified BCP-ALL-derived clonally-related IGH sequences by their shared 'DNJ-stem'. We introduce the concept of 'marker DNJ-stem' to cover the entirety of, even lowly abundant, clonally-related family members. In a cohort of 280 adult patients with BCP-ALL, IGH clonal evolution at diagnosis was identified in one-third of patients. The phenomenon was linked to contemporaneous recombinant and editing activity driven by aberrant ongoing DH/VH-DJH recombination and VH replacement, and we share insights and examples for both. Furthermore, in a subset of 167 patients with molecular subtype allocation, high prevalence and high degree of clonal evolution driven by ongoing DH/VH-DJH recombination were associated with the presence of KMT2A gene rearrangements, while VH replacements occurred more frequently in Ph-like and DUX4 BCP-ALL. Analysis of 46 matched diagnostic bone marrow and peripheral blood samples showed a comparable clonal and clonotypic distribution in both hematopoietic compartments, but the clonotypic composition markedly changed in longitudinal follow-up analysis in select cases. Thus, finally, we present cases where the specific dynamics of clonal evolution have implications for both the initial marker identification and the MRD monitoring in follow-up samples. Consequently, we suggest to follow the marker DNJ-stem (capturing all family members) rather than specific clonotypes as the MRD target, as well as to follow both VDJH and DJH family members since their respective kinetics are not always parallel. Our study further highlights the intricacy, importance, and present and future challenges of IGH clonal evolution in BCP-ALL.