Clonal Selection Research Articles

Innovative Solutions for IK: PROA and Clonal Selection Algorithms Unveiled

Calculating joint angles for sequential manipulators consists of studying the correlation between Cartesian and joint variables. The problem-solving technique encounters two main hurdles described as direct and inverse kinematics. Matrix multiplications usually simplify the direct kinematic problem. However, inverse kinematic problems are harder as they require solving many nonlinear equations and eliminating variables a lot. In our work, we introduce two new methods of handling the complicated inverse kinematic problem for robotic manipulator arms; Poor and Rich Optimization Algorithm and Clonal Selection Algorithm (CSA). These advanced techniques enhance greatly the estimation of various joints in the arm which makes the solution more precise and efficient. To demonstrate the effectiveness, robustness, and potential benefits of these approaches for complicated kinematic problems we present extensive simulation results thereby enabling better performance of robots.

Intraoperative imaging of residual ovarian cancer after neoadjuvant chemotherapy using indocyanine green

ObjectivesInterval debulking surgery has similar outcomes and less morbidity compared with primary debulking in advanced ovarian cancer. However, there is controversy regarding the selection of chemotherapy-resistant clones. Complete resection is...

Selective Clonal Regression After Interferon Therapy in Metastatic Melanoma.

Regression (total or partial) is a common phenomenon in melanoma. From a pathogenic perspective, it is highly complex and only partially understood, involving aspects of both the tumor and the individual. One of the determining factors is the clonal selection of the tumor, wherein some clones within the tumor survive while others perish. This clonal selection can sometimes occur as a selective mechanism after the initiation of a therapeutic intervention. In many of these cases, the effect is detrimental, because the surviving clone is resistant to the applied therapy. However, occasionally, the therapy can successfully select the less harmful clone. We present an example of the latter, where therapy with interferon induced regression of the metastatic-capable melanocytic population, with only the primary tumor melanocytic population persisting. To confirm this, we demonstrated BRAF mutational similarity between the 2 populations, and an additional NRAS mutation in the metastatic population, which was absent in the primary tumor.

Antiapoptosis Engineering for Improved Protein Production from CHO Cells.

Improving the time integral of viable cell concentration by overcoming cell death, namely apoptosis, is one of the most widely used strategies for the efficient production of therapeutic proteins. By establishing stable cell lines that overexpress antiapoptotic genes or downregulate proapoptotic genes, the final product yields can be enhanced as cells become more resistant to environmental stresses. From the selection of high-expressing clones to verification of antiapoptotic activity, the method to construct a stable antiapoptotic cell line is discussed in this chapter.

Leveraging AI to Automate Detection and Quantification of Extrachromosomal DNA (ecDNA) to Decode Drug Responses.

Traditional drug discovery efforts have largely focused on targeting rapid, reversible protein-mediated adaptations to undermine cancer cells' resistance to therapy. However, cancer cells also exploit DNA-based strategies, typically viewed as slow, irreversible, and unpredictable changes like point mutations or the selection of drug-resistant clones. Contrary to this perception, extrachromosomal DNA (ecDNA) represents a form of DNA alteration that is rapid, reversible, and predictable, playing a crucial role in cancer's adaptive response. In this study, we present a novel post-processing pipeline for the automated detection and quantification of ecDNA in Fluorescence in situ Hybridization (FISH) images using the Microscopy Image Analyzer (MIA) tool. Our approach is particularly designed to monitor ecDNA dynamics during drug treatment, providing a quantitative framework to understand how ecDNA enables cancer cells to swiftly and reversibly adapt to therapeutic pressure. This pipeline not only offers a valuable resource for researchers aiming to automate ecDNA detection in FISH images but also sheds light on the adaptive mechanisms of ecDNA in response to epigenetic remodeling agents like JQ1.

Compressive stresses in cancer: characterization and implications for tumour progression and treatment.

Beyond their many well-established biological aberrations, solid tumours create an abnormal physical microenvironment that fuels cancer progression and confers treatment resistance. Mechanical forces impact tumours across a range of biological sizes and timescales, from rapid events at the molecular level involved in their sensing and transmission, to slower and larger-scale events, including clonal selection, epigenetic changes, cell invasion, metastasis and immune response. Owing to challenges with studying these dynamic stimuli in biological systems, the mechanistic understanding of the effects and pathways triggered by abnormally elevated mechanical forces remains elusive, despite clear correlations with cancer pathophysiology, aggressiveness and therapeutic resistance. In this Review, we examine the emerging and diverse roles of physical forces in solid tumours and provide a comprehensive framework for understanding solid stress mechanobiology. We first review the physiological importance of mechanical forces, especially compressive stresses, and discuss their defining characteristics, biological context and relative magnitudes. We then explain how abnormal compressive stresses emerge in tumours and describe the experimental challenges in investigating these mechanically induced processes. Finally, we discuss the clinical translation of mechanotherapeuticsthat alleviate solid stresses and their potential to synergize with chemotherapy, radiotherapy and immunotherapies.

Emergence of IGH::CCND1 rearrangement and mutations in TP53, BTK, and BCL2 associated with therapy resistance in chronic lymphocytic leukemia

AbstractChronic lymphocytic leukemia (CLL) is an indolent low‐grade B‐cell neoplasm that generally responds well to treatment. Rarely, CLL cases exhibit an IGH::CCND1 rearrangement, presenting a diagnostic challenge in distinguishing between clonal evolution within CLL and an independent mantle cell lymphoma. We report a case of CLL with the emergence of an IGH::CCND1 rearrangement and mutations associated with treatment resistance, including TP53, BTK, and BCL2, during disease progression. Immunophenotypic, cytogenetic, and molecular analyses support that these alterations are secondary events within the CLL clone. This case demonstrates dynamic clonal selection and expansion in response to treatments, which, in turn, contributes to treatment resistance.

Developing a workflow for the isolation of hybridoma cells producing fully human antigen-specific antibodies using a surface IgG detection method

The antigen-mediated B cell isolation method, based on the detection of surface IgG (sIgG), has increased the efficiency of therapeutic antibody (Ab) discovery. However, the reduction in sIgG expression on B cells during plasma cell differentiation presents challenges as it enables Ab production from only a small subset of B cells (e.g., memory B cells). The present study aimed to addressed this problem by developing a workflow to isolate human-IgG-secreting hybridoma cells produced by cell fusion, the majority of which express sIgG. We showed that our sIgG-based antigen-coated bead separation method efficiently enriched hybridoma cells expressing antigen-specific Abs with a yield of 83.5% (from the cell fusion pool) and a positive rate of 73.2%. Furthermore, because the separation could be performed after only a short (1–2-day) culture period following cell fusion, diverse hybridoma clones could be obtained, minimizing clonal selection and the incidence of duplicates. Given that the expression of membrane-bound IgG and sIgG are regulated by different splicing mechanisms, we speculate that the cell fusion step potentially attenuated the suppression of human sIgG expression. Overall, our proposed method is expected to markedly improve the efficiency of therapeutic Ab candidate production, which will have important clinical implications.

Cytotoxicity, genotoxicity and mutagenicity of mixed ternary mononuclear Mg complex based on valproic acid with 1,10-phenanthroline in Saccharomyces cerevisiae and V79 cells.

Valproic acid (VA) is a widely used drug for the treatment of diseases affecting the central nervous system. Due to its epigenetic modulatory potential, it has been studied for possible therapeutic application in anticancer therapies. However, the VA exhibits different side effects in its application. Thus, synthetic coordination complexes with valproate can generate promising candidates for new active drugs with reduced toxicity. In this sense, we investigated the genotoxic and mutagenic potential of the sodium valproate and of the mixed ternary mononuclear Mg complex based on VA with 1,10-phenanthroline (Phen) ligand - [Mg (Valp)2Phen], in Saccharomyces cerevisiae and V79 cells. The MTT and clonal survival assays in V79 cells indicated that the Mg complex has higher cytotoxicity than sodium valproate. A similar cytotoxicity profile is observed in yeast. This fact is possibly due to the intercalation capacity of [Mg(Valp)2Phen], inducing DNA strand breaks, as observed in the comet assay and micronucleus test. In this sense, members of the NER, HR, NHEJ and TLS repair pathways are required for the repair of DNA lesions induced by [Mg(Valp)2Phen]. Interestingly, BER proteins apparently increase the cytotoxic potential of the drug. Furthermore, the [Mg(Valp)2Phen] showed higher cytotoxicity in V79 cells and yeast when compared to sodium valproate indicating applicability as a cytotoxic agent.

ADVANCING INFORMATION TECHNOLOGY WITH IMMUNOLOGICAL COMPUTING – SOFT COMPUTING TECHNIQUES FOR ADAPTIVE AND ROBUST SYSTEMS

The field of Information Technology (IT) is evolving rapidly, and with this growth comes the need for systems that are both adaptive and robust. Biological systems, especially the human immune system, demonstrate remarkable adaptability and resilience, inspiring the development of Immunological Computing (IC). This paper explores the application of immunological principles in Soft Computing techniques to create systems capable of responding to dynamic environments. Current IT systems often face challenges such as handling unpredictable changes, scalability, and security threats. Traditional computing approaches struggle to address these issues efficiently due to their rigid structures and limited adaptability. Immunological Computing, inspired by the immune system’s ability to learn, remember, and adapt, offers a promising solution. The proposed method integrates immune system mechanisms like clonal selection, immune memory, and self/non-self-recognition into computational models. These models are coupled with soft computing techniques such as fuzzy logic, genetic algorithms, and neural networks, enhancing the system’s ability to adapt to changing environments and uncertainties. In simulated tests, this approach demonstrated a significant improvement in robustness and adaptability compared to traditional IT systems. For instance, in a cybersecurity application, the immunological-based system detected and neutralized 94.6% of threats, a notable improvement over the 82.3% detected by conventional systems. Similarly, in a resource optimization scenario, the system adapted to dynamic workloads with an efficiency increase of 15% compared to static systems.

JAK2V617F-dependent down regulation of SHP-1 expression participates in the selection of myeloproliferative neoplasm cells in the presence of TGF-β.

Myeloproliferative neoplasms (MPNs) are characterized by an increased production of blood cells due to the acquisition of mutations such as JAK2V617F. TGF-β, whose secretion is increased in MPN patients, is known to negatively regulate haematopoietic stem cell (HSC) proliferation. Using an isogenic JAK2V617F or JAK2 wild-type UT-7 cell line we observed that JAK2V617F cells resist to TGF-β antiproliferative activity. Although TGF-β receptors and SMAD2/3 expressions are similar in both cell types, TGF-β-induced phosphorylation of SMAD2/3 is reduced in UT-7 JAK2V617F cells compared with JAK2 WT cells. We confirmed that JAK2V617F mutated cells are resistant to the antiproliferative effect of TGF-β in a competitive assay as we observed a positive selection of JAK2V617F cells when exposed to TGF-β. Using cell lines, CD34-positive cells from MPN patients and bone marrow cells from JAK2V617F knock-in mice we identified a down regulation of the SHP-1 phosphatase, which is required for the regulation of HSC quiescence by TGF-β. The transduction of SHP-1 cDNA (but not a phosphatase inactive cDNA) restores the antiproliferative effect of TGF-β in JAK2V617F mutated cells. Finally, SC-1, a known agonist of SHP-1, antagonized the selection of JAK2V617F mutated cells in the presence of TGF-β. In conclusion, we show a JAK2-dependent down regulation of SHP-1 in MPN patients' cells which is related to their resistance to the antiproliferative effect of TGF-β. This may participate in the clonal selection of cancer cells in MPNs.

Ovarian cancer-derived IL-4 promotes immunotherapy resistance.

Ovarian cancer is resistant to immunotherapy, and this is influenced by the immunosuppressed tumor microenvironment (TME) dominated by macrophages. Resistance is also affected by intratumoral heterogeneity, whose development is poorly understood. To identify regulators of ovarian cancer immunity, we employed a spatial functional genomics screen (Perturb-map), focused on receptor/ligands hypothesized to be involved in tumor-macrophage communication. Perturb-map recapitulated tumor heterogeneity and revealed that interleukin-4 (IL-4) promotes resistance to anti-PD-1. We find ovarian cancer cells are the key source of IL-4, which directs the formation of an immunosuppressive TME via macrophage control. IL-4 loss was not compensated by nearby IL-4-expressing clones, revealing short-range regulation of TME composition dictating tumor evolution. Our studies show heterogeneous TMEs can emerge from localized altered expression of cancer-derived cytokines/chemokines that establish immune-rich and immune-excluded neighborhoods, which drive clone selection and immunotherapy resistance. They also demonstrate the potential of targeting IL-4 signaling to enhance ovarian cancer response to immunotherapy.

Identification and fine mapping of a QTL-rich region for yield-and quality-related traits on chromosome 4BS in common wheat (Triticum aestivum L.).

Yield and quality are important for plant breeding. To better understand the genetic basis underlying yield- and quality-related traits in wheat (Triticum aestivum L.), we conducted the quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) and a high-density genetic linkage map with a 90K array. In this study, a total of 117 QTLs were detected for spike number per area (SNPA), thousand grain weight (TGW), grain number per spike (GNS), plant height (PH), spike length (SL), total spikelet number (TSN), spikelet density (SD), grain protein content (GPC), and grain starch content (GSC). Among these QTLs, 30 environmentally stable QTLs for yield- and quality-related traits were detected. Notably, five QTL-rich regions (Qrr) for yield-and/or quality-related traits were identified, including the QTL-rich region on chromosome 4BS (QQrr.cau-4B) for eight traits (SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC). The stable QTL-rich region QQrr.cau-4B was delimited into a physical interval of approximately 2.47Mb. Based on the annotation information of the Chinese spring wheat genome v1.0 and parental re-sequencing results, the interval included twelve genes with sequence variations. Taken together, these results contribute to further understanding of the genetic basis of SNPA, GNS, PH, SL, TSN, SD, GPC, and GSC, and fine mapping of QQrr.cau-4B will be beneficial for gene cloning and marker-assisted selection in the genetic improvement of wheat varieties.

Analysis of hybrid potato populations in the conditions of the Magadan region

The priority direction in potato breeding in the Magadan region, given the short growing season and heat shortage, is the creation of predominantly early-ripening potato varieties. The article presents the results of the evaluation of potato breeding samples in terms of productivity and ripeness. Over two years, about three thousand samples of 67 hybrid combinations have been studied. The research was carried out in 2022–2023 on the experimental field of the Magadan Scientific Research Institute of Agriculture on floodplain, sod-alluvial, pebble-sandy loam soils. More than two thousand samples represented by 25 hybrid combinations were studied in the nursery of seedlings. Hybrid combinations characterized by a high frequency of selection of promising forms are identified, such as Arctica × Elbeida, Udacha × Bellarosa, Krone × Bellarosa, Charoite × Bellarosa, Krone × Labadia, Arctica × Gala. In these hybrid combinations, from 7.6 to 17.9% of the samples from the total number of the seedlings planted in the field were selected as clones. The samples with high productivity indicators were selected in the nursery of hybrids of the 1st year. The maximum weight of tubers of one plant was noted in the populations of Columba × Krepysh – 2010, Udacha × Bellarosa – 1820, Arctica × Elbeida – 1825, Charoite × Bellarosa – 1800. In the nursery of hybrids of the 2nd year, hybrids with productivity exceeding 1000 g/bush, such as Columba × Krepysh (2700 g/bush), Udacha × Bellarosa (1950 g/bush), Arctica × Krepysh (1670 g/bush), were identified in terms of yield and economically valuable characteristics. The frequency of selection of productive clones here exceeded 50%. These hybrid combinations are recommended for breeding research in the conditions of the Magadan region.

The immune response formed by the introduction of a DNA vector containing a cDNA fragment of the human thyroid-stimulating hormone receptor gene into transgenic mice

The number of patients with autoimmune thyroid diseases (Graves’disease, Hashimoto’sthyroiditis) is increasing globally. The most important part in the diagnosis of Graves’ disease (GD) is the detection of autoantibodies to the thyrotropin receptor (TSHR) in Graves’ patients’ sera. For the differential diagnosis of antibodies to thyroid antigens, it is promising to use tests based on monoclonal antibodies to TSHR, which can be obtained not only as a result of immunization with native or recombinant TSHR protein, but also through DNA immunization with genetically engineered constructs containing fragments of the TSHR gene. Based on mRNA we isolated from the thyroid tissue in GD, a number of fragments of the thyrotropin receptor gene were cloned, suitable for DNA immunization of animals. The purpose of this work is to evaluate the immunogenic properties of one of the constructed vectors, pVAX1-TSHR (1160), in a mouse model. The successful inclusion of the extracellular domain gene fragment of the human TSHR (1160), which was transfected into CHO cells as a part of the pVAX1 vector was confirmed by immunoblotting and ELISA. The immune response formed to the injection of the pVAX1 vector into BALB/c mice, containing a fragment of the human TSHR gene, was detected in different versions of ELISA. Immunization of animals with the DNA vector pVAX1-TSHR according to an experimentally selected scheme was effective for the formation of mouse splenocytes, secreting antibodies to TSHR, which were used for successful hybridization. This was confirmed by the results of determining antibody production to TSHR in murine blood sera. The level of antibody production remained high (titer more than 1:10.000) at the 8th week of the experiment. As a result of selection of individual clones according to the criteria of proliferative activity and stability of antibody production, the most stable cultures secreting mAbs against TSHR were selected.

Agronomic features of introduced Argan tree in eastern of Morocco and optimization of their propagation

Argania spinosa or argan is an endemic plant of Morocco that belongs to sapotaceae family. This species has significant ecological and socioeconomical impact in Morocco and is mainly recognized by argan oil that is very known for its nutritional quality and health benefits. Our study aims to elaborate an agronomical and pomological characterization of introduced argan trees in Oujda, Morocco (about 200 trees, 10 years old) , select high-performance clone heads based on their productivity and stability criteria, by measuring various productivity parameters over a tree years study period (fresh fruit production, almonds production and oil production), and successfully propagate them asexually using apical grafting technique in controlled condition ( phytotron ) with the aim of stabilizing the high-performance clone. The obtained results indicated the existence of high diversity in terms of the various pomological parameters assessed. Parallelly, productivity and profitability parameters, the average production of fresh fruits, almonds and oil per tree and per year was 8.62 kg, 0.253 kg and 0.133 L, respectively. While, the maximal production was 34.4 kg/year for fresh fruits production, 1.07 kg/year/tree for almonds, and 0.575 liter/year/tree oil produced. Regarding the propagation of these clones, the results showed that the grafting success rate depended on the mother stock and the season, with 100% success rate. The results obtained show that the argan tree is an adaptive species, and the most suitable grafting method for the argan tree is apical split grafting during the autumn season.

Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients.

Whereas severe COVID-19 is often associated with elevated autoantibody titers, the underlying mechanism behind their generation has remained unclear. Here we report clonal composition and diversity of autoantibodies in humoral response to SARS-CoV-2. Immunoglobulin repertoire analysis and characterization of plasmablast-derived monoclonal antibodies uncovered clonal expansion of plasmablasts producing cardiolipin (CL)-reactive autoantibodies. Half of the expanded CL-reactive clones exhibited strong binding to SARS-CoV-2 antigens. One such clone, CoV1804, was reactive to both CL and viral nucleocapsid (N), and further showed anti-nucleolar activity in human cells. Notably, antibodies sharing genetic features with CoV1804 were identified in COVID-19 patient-derived immunoglobulins, thereby constituting a novel public antibody. These public autoantibodies had numerous mutations that unambiguously enhanced anti-N reactivity, when causing fluctuations in anti-CL reactivity along with the acquisition of additional self-reactivities, such as anti-nucleolar activity, in the progeny. Thus, potentially CL-reactive precursors may have developed multiple self-reactivities through clonal selection, expansion, and somatic hypermutation driven by viral antigens. Our results revealed the nature of autoantibody production during COVID-19 and provided novel insights into the origin of virus-induced autoantibodies.

Tracking Response and Resistance in Acute Myeloid Leukemia through Single-Cell DNA Sequencing Helps Uncover New Therapeutic Targets.

Acute myeloid leukemia (AML) is an aggressive hematologic neoplasia with a complex polyclonal architecture. Among driver lesions, those involving the FLT3 gene represent the most frequent mutations identified at diagnosis. The development of tyrosine kinase inhibitors (TKIs) has improved the clinical outcomes of FLT3-mutated patients (Pt). However, overcoming resistance to these drugs remains a challenge. To unravel the molecular mechanisms underlying therapy resistance and clonal selection, we conducted a longitudinal analysis using a single-cell DNA sequencing approach (MissionBioTapestri® platform, San Francisco, CA, USA) in two patients with FLT3-mutated AML. To this end, samples were collected at the time of diagnosis, during TKI therapy, and at relapse or complete remission. For Pt #1, disease resistance was associated with clonal expansion of minor clones, and 2nd line TKI therapy with gilteritinib provided a proliferative advantage to the clones carrying NRAS and KIT mutations, thereby responsible for relapse. In Pt #2, clonal architecture was less complex, and 1st line TKI therapy with midostaurin was able to eradicate the leukemic clones. Our results corroborate previous findings about clonal selection driven by TKIs, highlighting the importance of a deeper characterization of individual clonal architectures for choosing the best treatment plan for personalized approaches aimed at optimizing outcomes.

Cassava breeding: Classical to recent breeding approaches for food, industry and climate resilience

Cassava ranks as the fourth-most significant starchy root crop in underdeveloped countries in terms of future food and acting as a key source of income for small and marginal farmers. To meet the growing demands for food security and economic development, it is imperative to develop improved cassava varieties that offer higher yields, enhanced nutritional content, safer for consumption, greater resistance to diseases and climate change. The development of these improved varieties necessitates advancements in breeding techniques, leveraging both traditional methods and modern biotechnological tools. However, a major challenge in cassava breeding is heterozygous nature and the crop’s sparse flowering, which limits the potential for sexual reproduction, thereby constraining breeding efforts for predominantly clonal selection. The continuous clonal propagation impedes genetic diversity and the introduction of novel traits, narrowing the overall progress of breeding programs. Integrating genomic tools and accelerating the adoption of biotechnological advancements can overcome these limitations and expedite the development of superior cassava varieties. This review highlights the need of cassava breeding for addressing these challenges with conventional as well as with new breeding techniques with the aim to provide a comprehensive understanding of the current scenario and future directions of cassava breeding research. Key words: Climate change, CRISPR/Cas 9, New breeding techniques, PPD, speed breeding, Waxy cassava

Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis.

Hematopoietic stem cells are regulated by endothelial and mesenchymal stromal cells in the marrow niche1-3. Leukemogenesis was long believed to be solely driven by genetic perturbations in hematopoietic cells but introduction of genetic mutations in the microenvironment demonstrated the ability of niche cells to drive disease progression4-8. The mechanisms by which the stem cell niche induces leukemia remain poorly understood. Here, using cellular barcoding in zebrafish, we found that clones of niche endothelial and stromal cells are significantly expanded in leukemic marrows. The pro-angiogenic peptide apelin secreted by leukemic cells induced sinusoidal endothelial cell clonal selection and transcriptional reprogramming towards an angiogenic state to promote leukemogenesis in vivo. Overexpression of apelin in normal hematopoietic stem cells led to clonal amplification of the niche endothelial cells and promotes clonal dominance of blood cells. Knock-out of apelin in leukemic zebrafish resulted in a significant reduction in disease progression. Our results demonstrate that leukemic cells remodel the clonal and transcriptional landscape of the marrow niche to promote leukemogenesis and provide a potential therapeutic opportunity for anti-apelin treatment.