Biology subjects

Hammoudi, N.

Publications and source records attributed to Hammoudi, N..

8 recordsLinked to original sources

bioRxiv2024

T cell mediated impairment of epithelial integrity in Crohn's disease

T lymphocytes play a major role in intestinal homeostasis, with a particular impact on the balance between self-renewal and differentiation of intestinal epithelial cells (IECs). In Crohns disease (CD) patients, the intestinal mucosa is inflamed, epithelium permeability is increased, and IECs present compositional and functional defects. The role of T lymphocytes interactions with IECs in the physiopathology of CD remains in question. Here, we use a three-dimensional human autologous coculture model between purified intestinal organoids derived from primary tissues of CD and non-inflammatory control patients, and mucosal T lymphocytes extracted from the same location. We show that while in homeostatic context T cells support the proliferation and differentiation balance of organoids, mucosal T lymphocytes from CD patients present a high cytotoxicity against IECs. Importantly, this cytotoxicity is a persistent defect overtime in culture. Organoids also show defective intestinal stem cells (ISCs) proliferation and morphological changes. Single cell RNA sequencing after coculture highlights a general response of T cells to the epithelial microenvironment, and more particularly, an increase activation of a pro-inflammatory CD8+ T cells effector population in CD patients compared to controls. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC="FIGDIR/small/621219v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@78453aorg.highwire.dtl.DTLVardef@8f484org.highwire.dtl.DTLVardef@1ed0934org.highwire.dtl.DTLVardef@f75094_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

NAD+ biosynthesis as a collateral lethality target for precision oncology

Genomic deletion of tumor suppressor genes (TSG) often encompasses neighboring genes which may be members of multi-gene families encoding cell essential functions. These genomic events create targetable cancer-specific vulnerabilities, termed "collateral lethality" as illustrated by homozygous deletion of the glycolytic gene ENO1, which sensitizes glioblastoma (GBM) cells to inhibition of its paralog ENO2. Here, we sought to generalize the concept by validating a second multi-gene family in an unrelated metabolic pathway. Nicotinamide-nucleotide adenylyltransferase (NMNAT) is an essential and (unlike the more extensively studied NAMPT) non-bypassable step in NAD biosynthesis encoded by three paralogs, one of which, NMNAT1, is homozygously deleted as part of the 1p36 tumor suppressor locus in TCGA data of GBM, Cholangiocarcinoma and Hepatocellular carcinoma (with near zero expression of found in several other malignancies). In a glioma cell line (Gli56) with homozygous deletion of NMNAT1 expressing NMNAT2 and NMNAT3, shRNA-mediated knockdown of NMNAT2 is selectively toxic to Gli56 NMNAT1-deleted but not ectopically rescued cells. As NMNAT1 and NMNAT2 are predominantly localized in the nucleus and cytosol, respectively, these data suggest a functionally common pool of cytosolic and nuclear NAD+. Inducible shRNA-mediated extinction of NMNAT2 decreases NAD+ levels and selectively kills NMNAT1-deleted, but not NMNAT1-rescued cells in vitro and eradicates intracranial tumors in vivo. Thus, collateral lethality is a generalizable framework for the development of new classes of targeted agents with an informed clinical development path in cancer. Statement of significanceAn ongoing challenge in precision oncology is the translation of genomic data into actionable therapeutic opportunities with clear clinical benefit. We have demonstrated that genes homozygously deleted by virtue of chromosomal proximity to major tumor suppressor genes can confer cancer-specific vulnerabilities, termed "collateral lethality". While our previous work validated one such collateral lethality target in glycolysis, we now provide empirical in vitro and in vivo evidence that this concept applies to another deleted gene governing an altogether distinct biochemical pathway. The generalization of collateral lethality may expand the spectrum of molecular targets in cancer with a genomically-informed path for accurate clinical development.

cancer biology↗

bioRxiv2022

Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn's disease

Crohns disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridiales and the microscopic detection of filamentous structures close to the epithelium of Tnf {Delta}ARE mice pointed towards segmented filamentous bacteria (SFB), a commensal well-known to induce the maturation of Th17 cell-derived immune responses that is highly implicated in the pathogenesis of IBD. We show that the abundance of SFB strongly correlates with the severity of CD-like ileal inflammation in Tnf {Delta}ARE and SAMP/Yit mice. SFB mono-colonization of germ-free Tnf {Delta}ARE mice confirmed the causal link and resulted in severe ileo-colonic inflammation, characterized by elevated tissue levels of Tnf and Il-17, neutrophil infiltration and loss of Paneth and goblet cell function. Co-colonization of SFB in human-microbiota associated Tnf {Delta}ARE mice confirmed that SFB presence is indispensable for disease development. Screening of 412 ileal and colonic mucosal biopsies from IBD patients using previously published and newly designed human SFB-specific primer sets showed no presence of SFB in human tissue samples. Simulating the protective effect of exclusive enteral nutrition (EEN) by feeding SFB mono-colonized Tnf {Delta}ARE mice EEN-like purified diet antagonized SFB colonization and prevented disease development in Tnf {Delta}ARE mice, clearly demonstrating the important role of diet in modulating this IBD-related but murine pathobiont.

microbiology↗

bioRxiv2020

Geographic microevolution of Mycobacterium ulcerans sustains Buruli ulcer extension, Australia

The reason why severe cases of Buruli ulcers caused by Mycobacterium ulcerans are emerging in some South Australia counties has not been determined. In this study, we measured the diversity of M. ulcerans complex whole genome sequences (WGS) and reported a marker of this diversity. Using this marker as a probe, we compared WGS diversity in Buruli ulcer-epidemic South Australia counties versus non-epidemic Australian counties and further refined comparisons at the level of counties where severe Buruli ulcer cases have been reported. Analyzing 218 WGS (35 complete and 183 reconstructed WGS, including 174 Australian WGS) yielded 15 M. ulcerans complex genotypes, including three genotypes specific to Australia and one genotype specific to South Australia. A 1,068-bp PPE family protein gene exhibiting genotype-specific sequence variations was employed to further probe 13 minority clones hidden in sequence reads. The repartition of these clones significantly differed between South Australia and the rest of Australia. In addition, a significantly higher prevalence of 3/13 clones was observed in South Australia counties of the Mornington Peninsula, Melbourne and Bellarine Peninsula than in other South Australia counties. The data presented in this report suggest that the microevolution of three M. ulcerans complex clones drove the emergence of severe Buruli ulcer cases in some South Australia counties. Sequencing one specific PPE gene served to efficiently probe M. ulcerans complex clones. Further functional studies may balance the environmental adaptation and virulence of these clones.

evolutionary biology↗

bioRxiv2020

Screening anti-infectious molecules against Mycobacterium ulcerans: a step towards decontaminating environmental specimens.

Mycobacterium ulcerans, a non-tuberculous mycobacterium responsible for Buruli ulcer, is residing in poorly defined environmental niches in the vicinity of stagnant water points where very few isolates have been confirmed. In the perspective of culturing M. ulcerans from such contaminated environmental specimens, we tested the in vitro susceptibility of M. ulcerans CU001 strain co-cultivated with XTC cells to anti-infectious molecules registered in the French pharmacopoeia, using a standardised concentration, to find-out molecules inactive against M. ulcerans which could be incorporated in decontaminating solution. Of 116 tested molecules, 64 (55.1%] molecules including 34 (29.3%] antibiotics, 14 (12%] antivirals, 8 (6.8%] antiparasitic and 8 (6.8%] antifungals were ineffective against M. ulcerans CU001; leaving 52 molecules active against M. ulcerans CU001. Three such inactive antimicrobial molecules (oxytetracycline, polymyxin E and voriconazole] were then selected to make a decontamination solution shown to respect M. ulcerans CU001 viability. These three antimicrobials could be incorporated into a decontamination solution for the tentative isolation and culture of M. ulcerans from environmental samples.

microbiology↗

bioRxiv2020

Translocating Mycobacterium ulcerans: an experimental model.

Mycobacterium ulcerans is a non-tuberculous environmental mycobacterium responsible for extensive cutaneous and subcutaneous ulcers in mammals, named Buruli ulcer in patients. M. ulcerans has been seldom detected in the feces of mammals but not in patients, nevertheless the detection and isolation of M. ulcerans in animal feces does not feet with the current epidemiological schemes for the disease. Here using an experimental model in which rats were fed with 109 colony-forming units of M. ulcerans, we detected M. ulcerans in feces of challenged rats for two weeks and along their digestive tract for 10 days. M. ulcerans was further detected in the lymphatic system including cervical and axillary lymph nodes and the spleen, but not in any other tissue including the healthy and breached skin, 10 days post-challenge. These observations indicate that in some herbivorous mammals, M. ulcerans contamination by the digestive route may precede translocation and limited infection of the lymphatic tissues without systemic infection. These herbivorous mammals may be sources of M. ulcerans for exposed populations but are unlikely reservoirs for the pathogen.

microbiology↗

bioRxiv2019

Investigation of skin microbiota reveals Mycobacterium ulcerans-Aspergillus sp. trans-kingdom communication

BackgroundMycobacterium ulcerans secrete a series of non-ribosomal-encoded toxins known as mycolactones that are responsible for causing a disabling ulceration of the skin and subcutaneous tissues named Buruli ulcer. The disease is the sole non-contagion among the three most common mycobacterial diseases in humans. Direct contact with contaminated wetlands is a risk factor for Buruli ulcer, responsible for M. ulcerans skin carriage before transcutaneous inoculation with this opportunistic pathogen. Methodology and principal findingsIn this study, we analysed the bacterial and fungal skin microbiota in individuals exposed to M. ulcerans in Burkina Faso. We showed that M. ulcerans-specific DNA sequences were detected on the unbreached skin of 6/52 (11.5%) asymptomatic farmers living in Sindou versus 0/52 (0%) of those living in the non-endemic region of Tenkodogo. Then, we cultured the skin microbiota of asymptomatic M. ulcerans carriers and negative control individuals, all living in the region of Sindou. A total of 84 different bacterial and fungal species were isolated, 21 from M. ulcerans-negative skin samples, 31 from M. ulcerans-positive samples and 32 from both. More specifically, Actinobacteria, Aspergillus niger and Aspergillus flavus were significantly associated with M. ulcerans skin carriage. We further observed that in vitro, mycolactones induced spore germination of A. flavus, attracting the fungal network. ConclusionThese unprecedented observations suggest that interactions with fungi may modulate the outcome of M. ulcerans skin carriage, opening new venues to the understanding of Buruli ulcer pathology, prophylaxis and treatment of this still neglected tropical infection. Author summaryBuruli ulcer is a chronic infectious disease caused by the environmental opportunistic pathogen Mycobacterium ulcerans which secretes an exotoxin responsible for its pathogenicity. The reservoir and sources of M. ulcerans in the environment remain elusive and its mode of transmission is unclear. To acquire M. ulcerans infection, at least two conditions must be met, viable bacteria and a skin lesion as demonstrated by experimental animal models. In this study, we showed that M. ulcerans specific DNA sequences could be detected on the healthy skin of asymptomatic farmers living in one region of Burkina Faso where Buruli ulcer cases had already been reported, but not in Buruli ulcer-free regions, suggesting skin carriage after contacts with environmental sources. We also investigated the skin microbiota of M. ulcerans carriers and found significant associations of some bacteria and fungi with skin carriage of M. ulcerans. These associations may due to the effect of mycolactones on some fungi species. As we showed previously with Mucor circinelloides and here with Aspergillus flavus.

microbiology↗

bioRxiv2018

Eradication of ENO1-deleted Glioblastoma through Collateral Lethality

Inhibiting glycolysis remains an aspirational approach for the treatment of cancer. We recently demonstrated that SF2312, a natural product phosphonate antibiotic, is a potent inhibitor of the glycolytic enzyme Enolase with potential utility for the collateral lethality-based treatment of Enolase-deficient glioblastoma (GBM). However, phosphonates are anionic at physiological pH, limiting cell and tissue permeability. Here, we show that addition of pivaloyloxymethyl (POM) groups to SF2312 (POMSF) dramatically increases potency, leading to inhibition of glycolysis and killing of ENO1-deleted glioma cells in the low nM range. But the utility of POMSF in vivo is dose-limited by severe hemolytic anemia. A derivative, POMHEX, shows equipotency to POMSF without inducing hemolytic anemia. POMHEX can eradicate intracranial orthotopic ENO1-deleted tumors, despite sub-optimal pharmacokinetic properties. Taken together, our data provide in vivo proof-of-principal for collateral lethality in precision oncology and showcase POMHEX as a useful molecule for the study of glycolysis in cancer metabolism.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/331538_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@1b78ebcorg.highwire.dtl.DTLVardef@1fc0ccforg.highwire.dtl.DTLVardef@ad268corg.highwire.dtl.DTLVardef@1bdee32_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗