Genotype of PAX2-related disorders

Genotype of PAX2-related disorders correlates with kidney and ocular manifestations

PAX2-related disorders encompass renal coloboma syndrome (RCS) and hereditary focal segmental glomerulosclerosis (FSGS) type 7. We retrospectively analyzed 27 Korean patients with PAX2 pathogenic variants detected between 2004 and 2022 and conducted a literature review of 328 cases, including 301 previously reported. In our cohort, 19 had RCS, 4 had FSGS, and 4 had isolated congenital anomalies of the kidneys and urinary tract.

Patients were classified by variant type into predicted loss of function (pLoF) and non-pLoF variant groups, and by variant location into paired domain and other sites group. pLoF variants were predominantly associated with RCS, observed in 82% of patients in both our data (18 of 22, P = 0.017) and the literature (140 of 171, P < 0.001). Kidney failure developed in 52% of Korean patients at a median age of 14.5 years, with no difference in kidney survival between variant types.

However, the literature review indicated faster progression to kidney failure in patients with pLoF variants (11.0 vs. 24.0 years; pLoF, n = 138 vs. non-pLoF, n = 71; P = 0.002), with no significant difference by variant location. Ocular manifestations were more common, had earlier onset, and were more severe in the pLoF variants group in our cohort (P = 0.038). The literature confirmed a higher prevalence of ocular involvement in patients with pLoF variants (pLoF, n = 175 vs. non-pLoF, n = 88; P < 0.001) and in those with paired domain variants (P = 0.01). pLoF variants in PAX2 were associated with worse kidney and ocular outcomes.

These findings support genotype-phenotype correlations, contributing to tailored management in patients with PAX2-related disorders.In conclusion, the clinical phenotypes of PAX2 pathogenic variants, including RCS, FSGS, and isolated CAKUT, were highly variable. A clear genotype-phenotype correlation was observed in both kidney and ocular manifestations. The pLoF variants were predominantly associated with RCS and exhibited a worse kidney prognosis compared to the non-pLoF variants in literature reviews, although this was not significant in our study.

The kidney survival did not differ by variant location. The pLoF variants were also associated with more common occurrence, earlier onset, and severe ocular involvement, which was not confined to the optic disc. The ocular involvement was more common in paired domain variants than in other sites. These insights demonstrate the significant implications of the genotype-based analysis approach in facilitating targeted and expedited patient care.

PAX2 gene, renal coloboma syndrome, CAKUT, optic nerve hypoplasia, transcription factor, autosomal dominant, gene mutation, developmental disorder, nephropathy, optic disc anomaly, missense mutation, nonsense mutation, frameshift mutation, kidney malformation, syndromic disorder, congenital defect, genotype-phenotype correlation, molecular diagnosis, hereditary nephropathy, eye development

#PAX2, #RenalColobomaSyndrome, #CAKUT, #GeneticDisorder, #KidneyDisease, #OpticNerveHypoplasia, #GeneMutation, #AutosomalDominant, #CongenitalAnomalies, #MolecularGenetics, #HereditaryDisorders, #MissenseMutation, #FrameshiftMutation, #PediatricNephrology, #EyeDevelopment, #SyndromicDisorder, #PAX2Mutation, #Nephropathy, #GeneticCounseling, #RareDisease

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Genetic Plant Diversity

Loss of Genetic Plant Diversity Is Now Visible From Space

A new study combining satellite imagery with genetic analysis reveals that climate and land use changes are driving increased vegetation growth in Europe’s mountain regions, ultimately leading to a decline in the genetic diversity of medicinal plants such as Greek mountain tea.

Mountain regions are among the most biodiverse areas on Earth, hosting some of the richest and most varied ecosystems. However, these habitats are undergoing rapid and profound changes due to global environmental pressures.

Over the last 50 years, increasing temperatures and shifts in land use at high elevations have promoted the expansion of vigorous, competitive vegetation such as shrubs and trees, a phenomenon known as “mountain greening.” This encroachment is displacing the specialized, low-growing plant species that characterize open montane grasslands.

One such plant affected by this trend is Sideritis, a key component of Mediterranean montane grassland flora. Commonly known as Greek mountain tea, Sideritis includes several closely related species and is valued both by local communities and the pharmaceutical industry for its medicinal properties, particularly in treating respiratory and gastrointestinal ailments.

At the same time, the popular medicinal plant is an indicator of the health of open mountain habitats.

Genetic Diversity in Decline

As part of the recently published study, the research team investigated the effects of increasing greening on the genetic diversity of Sideritis, using an innovative methodological approach.

“We examined populations in eleven Greek mountain ranges and combined satellite data from several decades with genetic analyses of herbarium specimens from the 1970s and present-day plant samples,” explains study leader Spyros Theodoridis, a former research associate at the Senckenberg Biodiversity and Climate Research Center in Frankfurt, who now works at the National Observatory of Athens.

“The results show that in eight of the eleven mountain regions we studied, genetic diversity declined significantly during this period. In particularly affected regions, up to 20 percent of the genome of individual plants is now subject to inbreeding – an indication of declining population sizes.”

“The speed at which shrubs and trees are spreading in previously open grasslands can be directly linked to the decline in genetic diversity in Sideritis populations,” adds co-author David Nogués-Bravo, Professor at the University of Copenhagen, and continues:

“The genetic diversity of a species is crucial for its ability to adapt to environmental changes. If this diversity dwindles, resistance to disease, drought, or other stress factors decreases, which can lead to extinction in the long term.”

Satellite data reveals consequences of global warming

A special aspect of the study is that it combines two entirely different data sources – remote sensing by satellite and genomic analyses – thus allowing conclusions to be drawn about the development of plant populations over several decades: “This combination opens up new possibilities for biodiversity monitoring,” emphasizes Spyros Theodoridis and continues: “It allows us to use satellite images to identify indications of genetic changes in mountain ecosystems without having to genetically examine each individual population on site.”

Monitoring the loss of genetic diversity from space was previously considered impossible.

“However, our results show that the extent of genetic erosion can be predicted with surprisingly high accuracy based solely on the increase in vegetation density,” adds co-author Thomas Hickler, Professor at the Senckenberg Biodiversity and Climate Research Center.

“This renders our method particularly attractive for use in mountainous regions that are difficult to access or in areas where genetic monitoring has hardly been possible to date.” The study also underlines the importance of natural history collections, explains Marco Thines, co-author and Professor at Senckenberg Biodiversity and Climate Research Center.

“Without the historical plant specimens in herbaria, the direct comparison over a period of 50 years would not have been possible. These archives of nature are invaluable for biodiversity research.” The increasing greening of mountain regions due to global warming and the abandonment of traditional forms of cultivation is widespread around the world and is clearly evident from satellite images.

The researchers therefore recommend that conservation measures should be prioritized in areas that are most severely affected by mountain greening. “There is an urgent need for comparable studies with other species and in other regions,” concludes Theodoridis. “This will allow us to gain a comprehensive picture of how environmental changes are affecting the genetic basis of biodiversity – and how we can effectively counter this development.”

Genetics, Genomics, DNA sequencing, Gene expression, Genetic variation, Heredity, Chromosomes, Mutation, Genetic engineering, Genome editing, CRISPR-Cas9, Epigenetics, Genetic markers, Human genome, Inheritance, Genotype, Phenotype, Molecular biology, RNA, Bioinformatics

#Genetics, #Genomics, #DNA, #GeneExpression, #CRISPR, #Mutation, #GeneticEngineering, #Epigenetics, #GenomicsResearch, #MolecularBiology, #HumanGenome, #GeneticDisorders, #RNA, #Bioinformatics, #Inheritance, #Genotype, #Phenotype, #GenomeEditing, #GeneticVariation, #Heredity

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Human–Machine Interaction

Frequency-encoded eye tracking smart contact lens for human–machine interaction

Eye tracking techniques enable high-efficient, natural, and effortless human-machine interaction by detecting users’ eye movements and decoding their attention and intentions. Here, a miniature, imperceptible, and biocompatible smart contact lens is proposed for in situ eye tracking and wireless eye-machine interaction.

Employing the frequency encoding strategy, the chip-free and battery-free lens successes in detecting eye movement and closure. Using a time-sequential eye tracking algorithm, the lens has a great angular accuracy of <0.5°, which is even less than the vision range of central fovea. Multiple eye-machine interaction applications, such as eye-drawing, Gluttonous Snake game, web interaction, pan-tilt-zoom camera control, and robot vehicle control, are demonstrated on the eye movement model and in vivo rabbit.

Furthermore, comprehensive biocompatibility tests are implemented, demonstrating low cytotoxicity and low eye irritation. Thus, the contact lens is expected to enrich approaches of eye tracking techniques and promote the development of human-machine interaction technology.

Design and characterization of the eye-tracking SCL

Demonstrates the wide application potential of the proposed eye tracking SCL. By detecting the gazing direction, the SCL can calculate the real-time gazing point on the virtual screen, enabling the interaction with software, such as giving a like when appreciating Vincent van Gogh’s famous artwork The Starry Night. Robots also can be eye-controlled through the user-defined eye command input and execute multiple missions like vehicle movement and camera rotation.

With miniaturization and portability, the eye tracking system can be used in daily life and bring negligible burden to the user. 4 RF tags, integrated at the peripheral region of SCL, provided the backscattering signal for eye motion detection. The coil-shaped RF tags had different resonant frequency due to well-designed distinct structural parameters based on the mechanism of resistance-inductance-capacitance (RLC) resonator. The return loss (S11) curve, measured by a vector network analyzer (VNA) through a reading coil, provided insights into the response of the tags through wireless detection. The recognition of eye movement and closure was enabled by it. The equivalent impedance at the terminals of the reading coil is as follow.

human–machine interaction, user experience, artificial intelligence, machine learning, robotics, natural language processing, human-centered design, wearable technology, cognitive ergonomics, user interface, virtual reality, augmented reality, haptic feedback, automation, adaptive systems, brain–computer interface, multimodal interaction, intelligent agents, usability testing, human factors

#HumanMachineInteraction, #UXDesign, #ArtificialIntelligence, #MachineLearning, #Robotics, #NaturalLanguageProcessing, #HCI, #WearableTech, #UserInterface, #VirtualReality, #AugmentedReality, #HapticFeedback, #Automation, #AdaptiveSystems, #BrainComputerInterface, #MultimodalInteraction, #IntelligentSystems, #Usability, #HumanCenteredDesign, #CognitiveErgonomics

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Bone Metastasis

Targeting initial tumour–osteoclast spatiotemporal interaction to prevent bone metastasis

Bone is the most common site of metastasis, and although low proliferation and immunoediting at the early stage make existing treatment modalities less effective, the microenvironment-inducing behaviour could be a target for early intervention.

Here we report on a spatiotemporal coupling interaction between tumour cells and osteoclasts, and named the tumour-associated osteoclast ‘tumasteoclast’—a subtype of osteoclasts in bone metastases induced by tumour-migrasome-mediated cytoplasmic transfer. We subsequently propose an in situ decoupling–killing strategy in which tetracycline-modified nanoliposomes encapsulating sodium bicarbonate and sodium hydrogen phosphate are designed to specifically release high concentrations of hydrogen phosphate ions triggered by tumasteoclasts, which depletes calcium ions and forms calcium-phosphorus crystals.

This can inhibit the formation of migrasomes for decoupling and disrupt cell membrane for killing, thereby achieving early prevention of bone metastasis. This study provides a research model for exploring tumour cell behaviour in detail and a proof-of-concept for behaviour-targeting strategy.

bone metastasis, skeletal-related events, cancer spread to bone, osteolytic lesions, osteoblastic lesions, bone pain, bone resorption, bone remodeling, tumor microenvironment, bone-targeted therapy, bisphosphonates, denosumab, bone scan, radionuclide therapy, pathological fracture, spinal cord compression, metastatic breast cancer, metastatic prostate cancer, bone marrow involvement, cancer-induced bone disease

#BoneMetastasis, #CancerSpread, #SkeletalHealth, #BoneLesions, #BonePain, #BoneOncology, #TumorInBone, #BoneTherapy, #Osteolytic, #Osteoblastic, #BoneMarkers, #Bisphosphonates, #Denosumab, #BoneScan, #CancerResearch, #OncologyCare, #MetastaticCancer, #BoneComplications, #SpinalCompression, #CancerTreatment

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Y-chromosome-bearing sperm

Novel single-chain fragment variable antibody targeting plasma membrane epitopes on porcine Y-chromosome-bearing sperm

The aim of this study was to construct and produce a single-chain fragment variable (scFv) antibody targeting the plasma membrane epitope on porcine Y-chromosome-bearing sperm (Y-sperm). The hybridoma cloned from 4D1-E8 exhibited the highest specificity, and Y-sperm was used to generate the scFv gene. The expected combination of 450 bp (VH) and 300 bp (VL) resulted in a 795 bp scFv gene. The scFv gene was inserted into the pET22b expression vector and expressed in E. coli BL21 (DE3). The resulting H4:L4 clone produced a highly specific scFv antibody to Y-sperm. 

The reactivity of the H4:L4 scFv antibody to porcine Y-sperm was confirmed via ELISA and flow cytometry. The H4:L4 scFv antibody exhibited low cross-reactivity with X-sperm (4.14%). The soluble H4:L4 scFv antibody exhibited significantly less cross-reactivity with X-sperm than did the 4D1-E8 mAb (4.14% vs. 15.5%). However, H4:L4 scFv and the 4D1-E8 mAbs had high cross-reactivity with other conventional livestock semen. 

The scFv antibodies and mAbs were detected on the Y-sperm surface via immunofluorescence, and the fluorescence intensities were particularly strong on the plasma membranes of Y-sperm. In this study, the production of a scFv antibody against porcine Y-sperm was successful and represents a novel achievement. This scFv antibody had a high affinity for porcine Y-sperm. The soluble scFv antibody and mAb can be used to sort Y- and X-sperm in treatments involving porcine semen bearing X or Y chromosomes.

The successful application of sexed semen technology in livestock production has led to the third revolution of reproductive technology after artificial insemination and embryo transfer. In recent decades, several unsuccessful studies and many inoperative patents for the separation of sperm bearing X and Y chromosomes have emerged. Physical parameters, including density, surface charge, swimming velocity, and sex-specific antigens, have been employed in numerous attempts to differentiate between X-chromosome-bearing sperm (X-sperm) and Y-chromosome-bearing sperm (Y-sperm). 

Currently, there is one quantitative and reasonably accurate method for sexing mammalian sperm that involves individual separation and discrimination of X-sperm and Y-sperm via flow cytometry. In numerous mammalian species, flow cytometry has been implemented to separate sperm, and it has advanced to a stage that permits commercial applications. There are numerous deficiencies in this method, including its high cost, damage to sperm cells, decreased conception rate after artificial insemination, and low sperm dose per straw. 

Consequently, identifying a sperm sorting method that is simple, inexpensive, effective, and less damaging is imperative. In addition, sex sorting via flow cytometry was successful for the bovine production industry. The use of sex sorting technology in pig production systems offers many similar advantages. However, several factors currently limit the implementation of sexing technology in pigs. The anatomical and physiological features inherent to the female pig, together with the relatively low sperm output of the flow cytometer, are the main limitations to the widespread use of this technology in pig production systems. 

Therefore, it is extremely important to develop immunological methods that are effective, cost-effective, convenient, and cause less damage in the process of sorting sperm. Immunological sexing, an alternative semen sexing method, has been successful in bulls, but there have been few studies on this topic in pigs.

Initially, the investigation of immunological sexing requires the initial development of antibodies that are specific to porcine Y-sperm. The surface antigens and specific proteins of X- and Y-sperm differ from each other. Therefore, the ability to evaluate specific antibodies is widely recognized. Engineered antibodies have been generated through the application of recombinant DNA technology. The currently employed practices of animal immunization and hybridoma development can be replaced by a bacterial system that is capable of synthesizing and expressing virtually an infinite quantity of antibodies to nearly any antigen. 

Recombinant antibodies (rAbs) are generated using recombinant DNA technologies, and they can offer several advantages over polyclonal and monoclonal antibodies. The best-known antibody fragments are the antigen-binding fragment (Fab) and the even smaller single-chain variable fragment (scFv). The scFv format consists of the variable region of the heavy chain (VH) joined to the variable region of the light chain (VL) with a peptide linker. They are low-cost and easily produced. Additionally, recombinant antibody affinities can be genetically modified to facilitate their purification or immobilization for downstream applications. 

Producing a scFv antibody for porcine Y-sperm will be both intriguing and beneficial. Previous studies have successfully produced ScFv antibodies specifically for sperm. Thaworn et al. (2022) created a scFv antibody specific to Y-sperm in bovines, and this antibody was successfully applied to sex sorting of bovine semen. In addition, Samuel and Naz (2008) obtained anti-sperm scFv antibodies with defined antigen specificity in humans. Additionally, Soares and Barbosa (2008), for the production of a soluble monoclonal scFv, screened clones from Simental sperm cells via flow cytometry, and those that specifically bound to 40–60% of the cells were selected. 

However, scFv antibody production has not been investigated for porcine Y-sperm. The study of the production of specific scFv antibodies that target Y-sperm is of great interest for application in the pig production industry. A significant amount of interest has been given to the synthesis of specific scFv antibodies against Y-sperm for use in the pig production industry.

Therefore, the present study focused on producing hybridoma cells that produce mAbs and used them to construct a scFv antibody against male-specific sites on a plasma membrane epitope in porcine Y-sperm. Additionally, the effectiveness and specificity of an antigen-binding site in mAbs and scFv antibodies in capturing the plasma membrane of Y-sperm were validated.

Y-chromosome, genetic inheritance, male lineage, paternal ancestry, Y-DNA haplogroups, non-recombining region, genetic markers, STR analysis, SNP mutations, male-specific DNA, human evolution, Y-chromosome sequencing, paternal genealogy, chromosomal aberrations, forensic genetics, ancient DNA studies, molecular anthropology, male infertility genetics, sex determination, population genetics

#Ychromosome, #GeneticInheritance, #MaleLineage, #PaternalAncestry, #YDNA, #Haplogroups, #GeneticMarkers, #SNPs, #STRanalysis, #HumanEvolution, #MolecularAnthropology, #AncientDNA, #PopulationGenetics, #MaleInfertility, #ForensicGenetics, #SexDetermination, #ChromosomeResearch, #GenomicStudies, #GenealogyResearch, #GeneticsResearch

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Crohn’s Disease

Prominence of Microbiota to Predict Fibrous Stenosis in Crohn’s Disease

Purpose

Intestinal fibrous stenosis due to Crohn’s disease (CD) is highly prevalent. Although several clinical risk factors for fibrous stenosis have been identified, such as perianal fistulizing disease, small bowel disease location, and deep mucosal ulceration, predicting fibrous stenosis remains challenging. The intestinal microbiota plays a crucial role in the development and progression of CD. However, its role in intestinal fibrous stenosis is poorly understood. Leveraging a single-center cross-sectional study, we aimed to investigate the role of fecal microbiota in CD-associated fibrous stenosis.

Methods

Using metagenomic analysis, we examined the differences in fecal microbiota between CD patients with intestinal fibrous stenosis and those without stenosis. We identified specific microbiota and assessed their predictive accuracy for intestinal fibrous stenosis. Additionally, we explored functional differences in intestinal microbiota between the two groups.

Results

Our investigation of fecal samples revealed no significant differences in the gut microbiota structure between patients with fibrous stenosis and those without stenosis in CD. However, taxonomically, we found 70 taxa with significantly different abundance (p < 0.05) between the two groups. Furthermore, LEfSe analysis indicated that g_Bacteroides and g_Enterocloster could predict intestinal fibrous stenosis while p_Actinobacteria, c_Actinomycetia, c_Bacilli, o_Lactobacillales, f_Streptococcaceae and g_Streptococcus could predict CD without stenosis. Functional analysis revealed differential enrichment in five metabolic pathways at the KEGG pathway level in CD patients with fibrous stenosis, including sphingolipid metabolism, lipoic acid metabolism, and biosynthesis of neomycin, kanamycin and gentamicin. In the eggNOG database, we observed differences in four functional categories between the two groups, encompassing cellular process, signaling, and metabolism.

Conclusion

Fecal microbiota significantly impacted intestinal fibrous stenosis in CD. Although there were no significant differences in alpha and beta diversities, fibrous stenosis was associated with changes in microbiota composition and function, suggesting the potential of fecal microbiota in predicting CD-associated fibrous stenosis.

Crohn’s Disease, inflammatory bowel disease, gastrointestinal inflammation, abdominal pain, chronic diarrhea, autoimmune disorder, bowel obstruction, malnutrition, weight loss, fatigue, intestinal ulcers, colonoscopy, ileitis, flare-ups, immunosuppressants, corticosteroids, biologic therapy, surgical resection, gut microbiota, dietary management

#CrohnsDisease, #IBD, #GutHealth, #AutoimmuneDisease, #ChronicIllness, #Inflammation, #DigestiveHealth, #CrohnsWarrior, #IBDAwareness, #CrohnsAwareness, #InvisibleIllness, #ChronicPain, #CrohnsSupport, #Biologics, #HealthyGut, #NutritionMatters, #LivingWithCrohns, #CrohnsFlare, #BowelDisease, #CrohnsJourney

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Infection and Gastric Cancer

Comprehensive Analysis of Potential Common Pathogenic Mechanisms for COVID-19 Infection and Gastric Cancer

A growing body of data suggests that the prevalence of COVID-19 pneumonia in patients with stomach cancer is much higher than in the general population. However, these mechanisms are still not fully understood. After a thorough examination of shared differentially expressed genes (DEGs) for gastric cancer (GC) and COVID-19 pneumonia, we performed functional annotation, protein–protein interaction (PPI) networks, module design, and pivot gene identification. qPCR was used to verify the expression of hub genes in GC.

Finally, a pivotal gene transcription factor-gene regulatory network was created and validated. According to functional enrichment analysis, common genes are mainly enriched in biological processes such as extracellular matrix tissue and extracellular structural tissue. Finally, five genes were found to be pivotal genes in the pathogenesis of GC and COVID-19 pneumonia: BGN (biglycan), UBE2C (ubiquitin-conjugating enzymes 2C), SPP1 (secreted phosphoprotein 1), THBS2 (thrombospondin 2), and COL1A1 (type I collagen alpha 1). These shared pathways and pivotal genes could provide new insights for more mechanistic studies.

The prevalence of gastric cancer (GC), particularly in East Asian nations, continues to be a serious worldwide health issue. GC will be the sixth most often diagnosed cancer and the third-leading cause of cancer-related deaths worldwide in 2020, with more than 1,089,103 (5.6%) diagnoses and more than 768,000 (7.7%) fatalities worldwide. The regions with the highest incidence of GC are Northeast Asia, Central and South America, and Eastern Europe. Although H. pylori infection, smoking, alcohol consumption, a high-salt diet, and physical inactivity are now widely acknowledged as independent risk factors for GC, the pathophysiology of the disease is still unknown for the majority of patients.

Investigating the shared transcriptional signature between GC and COVID-19 pneumonia may reveal fresh information about the shared etiology of these two illnesses. We wanted to find important genes connected to the etiology of GC concomitant with COVID-19 pneumonia in this investigation. We analyzed the dataset downloaded from the GEO database. Common differentially expressed genes (DEGs) and their roles in COVID-19 pneumonia and GC were discovered using integrated bioinformatics and enrichment analysis. 

The STRING (Search Tool for Retrieving Interacting Gene) database and Cytoscape software (version 3.10.1) were also used to evaluate gene modules and find pivotal genes, which was followed by the confirmation of the pivotal genes. Finally, we selected 15 crucial essential genes, confirmed them, and further developed a TF-gene regulatory network for these genes. It is anticipated that the key genes between COVID-19 pneumonia and GC discovered in this work may reveal fresh details about the biological underpinnings of these two disorders.

gastric cancer, stomach cancer, adenocarcinoma, H. pylori infection, gastric tumors, cancer staging, chemotherapy, radiation therapy, targeted therapy, immunotherapy, gastrectomy, early detection, gastric biopsy, tumor markers, cancer prognosis, gastric ulcer, cancer metastasis, gastric mucosa, palliative care, oncology research

#GastricCancer, #StomachCancer, #CancerAwareness, #Oncology, #HelicobacterPylori, #CancerResearch, #CancerTreatment, #EarlyDetection, #Chemotherapy, #RadiationTherapy, #TargetedTherapy, #Immunotherapy, #Gastrectomy, #CancerSurvivor, #CancerCare, #TumorBiology, #PalliativeCare, #Gastroenterology, #CancerSupport, #MedicalResearch

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