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Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

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Animal Models and Experimental Medicine 2024年第1期7卷 36-47页

作者： Roa'a H.S.Yosief Iqbal M.Lone Aharon Nachshon Heinz Himmelbauer Irit Gat-Viks fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael School of Molecular Cell Biology and Biotechnology George S.Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael Institute of Computational Biology Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 181190 ViennaAustria

Background:Aspergillus fumigatus(Af)is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic back-ground.The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus(Af)using an RNAseq approach in CC lines and hepatic gene expression.Methods:We studied 31 male mice from 25 CC lines at 8 weeks old;the mice were infected with Af.Liver tissues were extracted from these mice 5 days post-infection,and next-generation RNA-sequencing(RNAseq)was performed.The GENE-E analysis platform was used to generate a clustered heat map matrix.Results:Significant variation in body weight changes between CC lines was ob-served.Hepatic gene expression revealed 12 top prioritized candidate genes differ-entially expressed in resistant versus susceptible mice based on body weight changes.Interestingly,three candidate genes are located within genomic intervals of the previ-ously mapped quantitative trait loci(QTL),including Gm16270 and Stox1 on chromo-some 10 and Gm11033 on chromosome 8.Conclusions:Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af.As a next step,eQTL analysis will be performed for our RNA-Seq data.Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

关键词： aspergillus fumigatus infection collaborative cross(CC)mice gene expression profile gene-network host susceptibility quantitative trait loci(QTL)mapping RNA-Seq

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Lowering fasting blood glucose with non-dialyzable material of cranberry extract is dependent on host genetic background,sex and diet

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Animal Models and Experimental Medicine 2023年第3期6卷 196-210页

作者： Fatima Amer-Sarsour Rana Tarabeih Itzhak Ofek fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael

Background:Type 2 diabetes(T2D)is a polygenic metabolic disease,character-ized by high fasting blood glucose(FBG).The ability of cranberry(CRN)fruit to regulate glycemia in T2D patients is well known.Here,a cohort of 13 lines of the genetically diverse Collaborative Cross(CC)mouse model was assessed for the effect of non-dialyzable material(NDM)of cranberry extract in lowering fasting blood glucose.Methods:Eight-week-old mice were maintained on either a standard chow diet(con-trol group)or a high-fat diet(HFD)for 12 weeks,followed by injections of intraperi-toneal(IP)NDM(50 mg/kg)per mouse,three times a week for the next 6 weeks.Absolute FBG(mg/dl)was measured bi-weekly and percentage changes in FBG(%FBG)between weeks 0 and 12 were calculated.Results:Statistical analysis showed a significant decrease in FBG between weeks 0 and 12 in male and female mice maintained on CHD.However,a non-significant in-crease in FBG values was observed in male and female mice maintained on HFD dur-ing the same period.Following administration of NDM during the following 6 weeks,the results show a variation in significant levels of FBG lowering between lines,male and female mice and under the different diets.Conclusion:The results suggest that the efficacy of NDM treatment in lowering FGB depends on host genetic background(pharmacogenetics),sex of the mouse(phar-macosex),and diet(pharmacodiet).All these results support the need for follow-up research to better understand and implement a personalized medicine approach/uti-lization of NDM for reducing FBG.

关键词： chow diet(CHD) collaborative cross(CC)mouse model fasting blood glucose(FBG) high-fat diet(HFD) non-dialyzable material(NDM)of cranberry extract type 2 diabetes(T2D)

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A study of the influence of genetic variance and sex on the density and thickness of the calvarial bone in collaborative cross mice

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动物模型与实验医学(英文) 2023年第4期6卷 355-361页

作者： Uriel Kaspersky Roei Levy Aysar Nashef fuad a.iraqi Yankel Gabet Department of Anatomy and Anthropology Tel Aviv UniversityTel AvivIsrael Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel Aviv UniversityTel Aviv69978Israel Department of Oral and Maxillofacial Surgery Baruch Padeh medical centerPoriyaIsrael

Background:Bone microarchitecture is affected by multiple genes,each having a small effect on the external appearance.It is thus challenging to characterize the genes and their specific effect on bone thickness and porosity.The purpose of this study was to assess the heritability and the genetic variation effect,as well as the sex effect on the calvarial bone thickness(Ca.Th)and calvarial porosity(%PoV)using the Collaborative Cross(CC)mouse population.Methods:In the study we examined the parietal bones of 56 mice from 9 lines of CC mice.Morphometric parameters were evaluated using microcomputed tomography(μCT)and included Ca.Th and%PoV.We then evaluated heritability,genetic versus environmental variance and the sex effect for these parameters.Results:Our morphometric analysis showed that Ca.Th and%PoV are both significantly different among the CC lines with a broad sense heritability of 0.78 and 0.90,respectively.The sex effect within the lines was significant in line IL111 and showed higher values of Ca.Th and%PoV in females compared to males.In line IL19 there was a borderline sex effect in Ca.Th in which males showed higher values than females.Conclusions:These results stress the complexity of sex and genotype interactions controlling Ca.Th and%PoV,as the skeletal sexual dimorphism was dependent on the genetic background.This study also shows that the CC population is a powerful tool for establishing the genetic effect on these traits.

关键词： calvarial porosity(%PoV) calvarial thickness(Ca.Th) collaborative cross mouse population diploe heritability sex effect

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Towards system genetics analysis of head and neck squamous cell carcinoma using the mouse model,cellular platform,and clinical human data

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Animal Models and Experimental Medicine 2023年第6期6卷 537-558页

作者： Osayd Zohud Iqbal M.Lone Aysar Nashef fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel AvivIsrael Department of Oral and Maxillofacial Surgery Baruch Padeh Medical CenterPoriyaIsrael Azrieli Faculty of Medicine Bar-Ilan UniversityRamat GanIsrael

Head and neck squamous cell cancer(HNSCC)is a leading global malignancy.Every year,More than 830000 people are diagnosed with HNSCC globally,with more than 430000 fatalities.HNSCC is a deadly diverse malignancy with many tumor locations and biological characteristics.It originates from the squamous epithelium of the oral cavity,oropharynx,nasopharynx,larynx,and hypopharynx.The most frequently impacted regions are the tongue and larynx.Previous investigations have demonstrated the critical role of host genetic susceptibility in the progression of HNSCC.Despite the advances in our knowledge,the improved survival rate of HNSCC patients over the last 40 years has been limited.Failure to identify the molecular origins of development of HNSCC and the genetic basis of the disease and its biological heterogeneity impedes the development of new therapeutic methods.These results indicate a need to identify more genetic factors underlying this complex disease,which can be better used in early detection and prevention strategies.The lack of reliable animal models to investigate the underlying molecular processes is one of the most significant barriers to understanding HNSCC tumors.In this report,we explore and discuss potential research prospects utilizing the Collaborative Cross mouse model and crossing it to mice carrying single or double knockout genes(e.g.Smad 4 and P53 genes)to identify genetic factors affecting the development of this complex disease using genome-wide association studies,epigenetics,micro RNA,long noncoding RNA,lnc RNA,histone modifications,methylation,phosphorylation,and proteomics.

关键词： animal models Collaborative Cross mice genomics head and neck squamous cell cancinoma host genetic susceptibility

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High-fat diet and oral infection induced type 2 diabetes and obesity development under different genetic backgrounds

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Animal Models and Experimental Medicine 2023年第2期6卷 131-145页

作者： Iqbal M.Lone Nadav Ben Nun Aya Ghnaim Arne S.Schaefer Yael Houri-Haddad fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael Department of Periodontology and Synoptic Dentistry Institute for Dental Craniofacial SciencesCharite-University of MedicineBerlinGermany Department of Prosthodontics Dental SchoolThe Hebrew UniversityJerusalemIsrael

Background:Type 2 diabetes(T2D)is an adult-onset and obese form of diabetes caused by an interplay between genetic,epigenetic,and environmental components.Here,we have assessed a cohort of 11 genetically different collaborative cross(CC)mouse lines comprised of both sexes for T2D and obesity developments in response to oral infection and high-fat diet(HFD)challenges.Methods:Mice were fed with either the HFD or the standard chow diet(control group)for 12 weeks starting at the age of 8 weeks.At week 5 of the experiment,half of the mice of each diet group were infected with Porphyromonas gingivalis and Fusobacterium nucleatum bacteria strains.Throughout the 12-week experimental period,body weight(BW)was recorded biweekly,and intraperitoneal glucose tolerance tests were performed at weeks 6 and 12 of the experiment to evaluate the glucose tolerance status of mice.Results:Statistical analysis has shown the significance of phenotypic variations between the CC lines,which have different genetic backgrounds and sex effects in different experimental groups.The heritability of the studied phenotypes was estimated and ranged between 0.45 and 0.85.We applied machine learning methods to make an early call for T2D and its prognosis.The results showed that classification with random forest could reach the highest accuracy classification(ACC=0.91)when all the attributes were used.Conclusion:Using sex,diet,infection status,initial BW,and area under the curve(AUC)at week 6,we could classify the final phenotypes/outcomes at the end stage of the experiment(at 12 weeks).

关键词： collaborative cross genetic covariance heritability high-fat diet machine learning mouse model obesity type 2 diabetes

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Impact of host genetics on gut microbiome: Take-home lessons from human and mouse studies

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Animal Models and Experimental Medicine 2020年第3期3卷 229-236页

作者： Inbal Cahana fuad a.iraqi Department of Human Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael

The intestinal microbiome has emerged as an important component involved in various diseases.Therefore,the interest in understanding the factors shaping its composition is growing.The gut microbiome,often defined as a complex trait,contains diverse components and its properties are determined by a combination of external and internal effects.Although much effort has been invested so far,it is still difficult to evaluate the extent to which human genetics shape the composition of the gut microbiota.However,in mouse studies,where the environmental factors are better controlled,the effect of the genetic background was significant.The purpose of this paper is to provide a current assessment of the role of human host genetics in shaping the gut microbiome composition.Despite the inconsistency of the reported results,it can be estimated that the genetic factor affects a portion of the microbiome.However,this effect is currently lower than the initial estimates,and it is difficult to separate the genetic influence from the environmental effect.Additionally,despite the differences between the microbial composition of humans and mice,results from mouse models can strengthen our knowledge of host genetics underlying the human gut microbial variation.

关键词： host genetic background intestinal microbiome in human and mouse microbial variations and profiles take-home lessons

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Strategies for generating mouse model resources of human disease

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Protein & Cell 2023年第12期14卷 866-870页

作者： Jirong Pan Ling Zhang Zhibing Huang Dalu Zhao He Li Yanan Fu Meng Wang Borui Chen fuad a.iraqi Grant Morahan Chuan Qin National Human Diseases Animal Model Resource Center NHC Key Laboratory of Human Disease Comparative MedicineBeijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious DiseasesBeijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesInstitute of Laboratory Animal SciencesCAMS&PUMCNational Center of Technology Innovation for Animal ModelChangping National Laboratory(CPNL)Beijing 102206China Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityRamat AvivTel Aviv 69978Israel Harry Perkins Institute of Medical Research QEII Medical Centre and Centre for Medical ResearchUniversity of Western AustraliaNedlandsPerthWA 6009Australia

The number of genetically modified mouse models that mimic human disease is growing rapidly,but only a tiny fraction has been commonly used.According to The Knockout Mouse Program(Lloyd,2011),a public resource of mouse embryonic stem cells containing a null mutation in every gene in the mouse genome,8,916 mutant mice lines were phenotyped up to 19 July 2022.Due to the poor correlation between the genomic responses in the mouse models and those responses in human disease,and since humans differ significantly in their genetic vulnerability to common diseases,we still need better mouse models,especially for common and chronic human diseases,including cancer,pulmonary and cardiovascular diseases,obesity and diabetes,behavioral disorders,and neurodegenerative diseases.These new models will be placed into a public repository,The China National Human Disease Animal Model Resource Center(NAMR).This project is funded by Ministry of Science and Technology of China and specializes in the creation,introduction,collection,preservation,and supply of animal model resources forhuman diseases.

关键词： diseases cardiovascular generating

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Efficient protocols and methods for high-throughput utilization of the Collaborative Cross mouse model for dissecting the genetic basis of complex traits

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Animal Models and Experimental Medicine 2019年第3期2卷 137-149页

作者： Hanifa J.Abu-Toamih Atamni fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of Medicine Tel Aviv University

The Collaborative Cross(CC)mouse model is a next‐generation mouse genetic reference population(GRP)designated for a high‐resolution quantitative trait loci(QTL)mapping of complex traits during health and disease.The CC lines were generated from reciprocal crosses of eight divergent mouse founder strains composed of five classical and three wild‐derived strains.Complex traits are defined to be controlled by variations within multiple genes and the gene/environment interactions.In this article,we introduce and present variety of protocols and results of studying the host response to infectious and chronic diseases,including type 2 diabetes and metabolic diseases,body composition,immune response,colorectal cancer,susceptibility to Aspergillus fumigatus,Klebsiella pneumoniae,Pseudomonas aeruginosa,sepsis,and mixed infections of Porphyromonas gingivalis and Fusobacterium nucleatum,which were conducted at our laboratory using the CC mouse population.These traits are observed at multiple levels of the body systems,including metabolism,body weight,immune profile,susceptibility or resistance to the development and progress of infectious or chronic diseases.Herein,we present full protocols and step‐by‐step methods,implemented in our laboratory for the phenotypic and genotypic characterization of the different CC lines,mapping the gene underlying the host response to these infections and chronic diseases.The CC mouse model is a unique and powerful GRP for dissecting the host genetic architectures underlying complex traits,including chronic and infectious diseases.

关键词： Collaborative Cross(CC)mouse model complex traits genetic reference population(GRP),infectious and chronic diseases quantitative trait loci(QTL)

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Assessing the host genetic background effects on type 2 diabetes and obesity development in response to mixed–oral bacteria and high-fat diet using the collaborative cross mouse model

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Animal Models and Experimental Medicine 2020年第2期3卷 152-159页

作者： Luna Karkar Hanifa JAbu-Toamih Atamni Asal Milhem Yael Houri-Haddad fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel AvivIsrael Department of Prosthodontics Dental SchoolHebrew UniversityHadassah JerusalemIsrael

Background: Host genetic background and sex, play central roles in defining the pathogenesis of type 2 diabetes(T2 D), obesity and infectious diseases. Our previous studies demonstrated the utilization of genetically highly diverse inbred mouse lines, namely collaborative cross(CC), for dissecting host susceptibility for the development of T2 D and obesity, showing significant variations following high-fat(42% fat) diet(HFD). Here, we aimed to assessing the host genetic background and sex effects on T2 D and obesity development in response to oral-mixed bacterial infection and HFD using the CC lines.Materials and Methods: Study cohort consists of 97 mice from 2 CC lines(both sexes), maintained on either HFD or Standard diet(CHD) for 12 weeks. At week 5 a group of mice from each diet were infected with Porphyromonas gingivalis(Pg) and Fusobacterium nucleatum(Fn) bacteria(control groups without infection). Body weight(BW) and glucose tolerance ability were assessed at the end time point of the experiment.Results: The CC lines varied(P <.05) at their BW gain and glucose tolerance ability(with sex effect) in response to diets and/or infection, showing opposite responses despite sharing the same environmental conditions. The combination of diet and infection enhances BW accumulation for IL1912, while restraints it for IL72. As for glucose tolerance ability, only females(both lines) were deteriorated in response to infection.Conclusions: This study emphasizes the power of the CC mouse population for the characterization of host genetic makeup for defining the susceptibility of the individual to development of obesity and/or impaired glucose tolerance.

关键词： collaborative cross(CC)mouse model high-fat diet(HFD) mixed oral bacteria(PG and Fn) obesity sex-differences type 2 diabetes(T2D)

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Studying host genetic background effects on multimorbidity of intestinal cancer development,type 2 diabetes and obesity in response to oral bacterial infection and high-fat diet using the collaborative cross(CC)lines

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Animal Models and Experimental Medicine 2021年第1期4卷 27-39页

作者： Asal Milhem Hanifa J.Abu Toamih-Atamni Luna Karkar Yael Houri-Haddad fuad a.iraqi Department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel AvivIsrael Department of Prosthodontics Dental SchoolThe Hebrew UniversityHadassah JerusalemIsrael

Background:Multimorbidity of intestinal cancer(IC),type 2 diabetes(T2D)and obesity is a complex set of diseases,affected by environmental and genetic risk factors.High-fat diet(HFD)and oral bacterial infection play important roles in the etiology of these diseases through inflammation and various biological mechanisms.Methods:To study the complexity of this multimorbidity,we used the collaborative cross(CC)mouse genetics reference population.We aimed to study the multimorbidity of IC,T2D,and obesity using CC lines,measuring their responses to HFD and oral bacterial infection.The study used 63 mice of both sexes generated from two CC lines(IL557 and IL711).For 12 weeks,experimental mice were maintained on specific dietary regimes combined with co-infection with oral bacteria Porphyromonas gingivalis and Fusobacterium nucleatum,while control groups were not infected.Body weight(BW)and results of a intraperitoneal glucose tolerance test(IPGTT)were recorded at the end of 12 weeks,after which length and size of the intestines were assessed for polyp counts.Results:Polyp counts ranged between 2 and 10 per CC line.The combination of HFD and infection significantly reduced(P<.01)the colon polyp size of IL557 females to 2.5 cm 2,compared to the other groups.Comparing BW gain,IL557 males on HFD gained 18 g,while the females gained 10 g under the same conditions and showed the highest area under curve(AUC)values of 40000-45000(min mg/dL)in the IPGTT.Conclusion:The results show that mice from different genetic backgrounds respond differently to a high fat diet and oral infection in terms of polyp development and glucose tolerance,and this effect is gender related.

关键词： high-fat diet(42%fat) intestinal cancer multimorbidity obesity oral bacterial infection type 2 diabetes(T2D)

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