Biology subjects

Bischoff, A.

Publications and source records attributed to Bischoff, A..

5 recordsLinked to original sources

bioRxiv2024

Isolation and characterization of microbiota from human pancreatic tumors and small intestine

Pancreatic ductal adenocarcinoma has a unique tumor microbiome and the systemic depletion of bacteria or fungi using antibiotic/antifungal cocktails leads to a decrease in pancreatic tumor burden in mice. However, functional studies remain rare due to the limited availability of clinically relevant microbiota. Here, we describe in detail the isolation of bacteria and fungi from the small intestine and tumor of pancreatic cancer patients at the Rogel Cancer Center. We then further characterized the impact of a newly isolated Klebsiella oxytoca strain (UMKO1) on the pancreatic tumor microenvironment using bacterial genome sequencing, untargeted and targeted metabolomics, as well as an ex vivo tumor transplant system. We found that UMKO1 possesses a gene for the long form of cytidine deaminase, which can inactivate the standard PDAC chemotherapeutic agent gemcitabine. In addition, we found that UMKO1 can produce several indoles when grown in tumor-like conditions, metabolites that can lead to an immune suppressive environment and interfere with therapy outcome. To test this in detail, we assessed changes in immune populations in pancreatic tumor explants upon exposure to the supernatant of UMKO1 and other isolated bacteria grown in tumor Interstitial fluid media (TIFM). We found that while none of the bacterial supernatants changed the abundance of CD8 T cells, granzyme B positive CD8 T cells were the lowest in tumor explants exposed to UMKO1, and not other isolated Klebsiella species or the non-pathogenic laboratory strain E. coli K12. In summary, the isolated collection of bacteria and fungi from this study are a valuable toolbox to study the impact of microbiota on pancreatic cancer.

cancer biology↗

bioRxiv2024

The role of chloroplast SRP54 domains and its C-terminal tail region in post- and cotranslational protein transport in vivo

In the chloroplast, the 54 kDa subunit of the signal recognition particle (cpSRP54) is involved in the posttranslational transport of the light-harvesting chlorophyll a/b-binding proteins (LHCPs) and the cotranslational transport of plastid-encoded subunits of the photosynthetic complexes to the thylakoid membrane. It forms a high-affinity complex with plastid-specific cpSRP43 for posttranslational transport, while a ribosome-associated pool coordinates its cotranslational function. CpSRP54 constitutes a conserved multidomain protein, comprising a GTPase (NG) and a methionine-rich (M) domain linked by a flexible region. It is further characterized by a plastid-specific C-terminal tail region containing the cpSRP43-binding motif. To characterize the physiological role of the various regions of cpSRP54 in thylakoid membrane protein transport, we generated Arabidopsis thaliana cpSRP54 knockout (ffc1-2) lines producing truncated cpSRP54 variants or a GTPase point mutation variant. Phenotypic characterization of the complementation lines demonstrated that the C-terminal tail region of cpSRP54 plays an important role specifically in posttranslational LHCP transport. Furthermore, we show that the GTPase activity of cpSRP54 plays an essential role in the transport pathways for both nuclear-as well as plastid-encoded proteins. In addition, our data revealed that plants expressing cpSRP54 without the C-terminal region exhibit a strongly increased accumulation of a photosystem I assembly intermediate. HighlightThis study elucidates the important role of the chloroplast SRP subunit, cpSRP54, in the biogenesis of both the LHC antenna and the cores of photosystem I and II in vivo.

plant biology↗

bioRxiv2023

Plant geographic distribution influences chemical defenses in native and introduced Plantago lanceolata populations

Plants growing outside their native range may be confronted by new regimes of herbivory, but how this affects plant chemical defense profiles has rarely been studied. Using Plantago lanceolata as a model species, we investigated whether introduced populations show significant differences from native populations in several growth and chemical defense traits. Plantago lanceolata (ribwort plantain) is an herbaceous plant species native to Europe and Western Asia that has been introduced to numerous countries worldwide. We sampled seeds from nine native and ten introduced populations that covered a broad geographic and environmental range and performed a common garden experiment in a greenhouse, in which we infested half of the plants in each population with caterpillars of the generalist herbivore Spodoptera littoralis. We then measured size-related and resource-allocation traits as well as the levels of constitutive and induced chemical defense compounds in roots and shoots of P. lanceolata. When we considered the environmental characteristics of the site of origin, our results revealed that populations from introduced ranges were characterized by an increase of chemical defense compounds without compromising plant biomass. The concentrations of iridoid glycosides and verbascoside, the major anti-herbivore defense compounds of P. lanceolata, were higher in introduced populations than in native populations. In addition, introduced populations exhibited greater rates of herbivore-induced volatile organic compound emission and diversity, and similar chemical diversity based on untargeted analyses of leaf methanol extracts. In general, the geographic origin of the populations had a significant influence on morphological and chemical plant traits, suggesting that P. lanceolata populations are not only adapted to different environments in their native range, but also in their introduced range.

ecology↗

bioRxiv2022

Arginase 1 is a key driver of immune suppression in pancreatic cancer

An extensive fibroinflammatory stroma rich in macrophages is a hallmark of pancreatic cancer. In this disease, it is well appreciated that macrophages are immunosuppressive and contribute to the poor response to immunotherapy; however, the mechanisms of immune suppression are complex and not fully understood. Immunosuppressive macrophages are classically defined by expression of the enzyme Arginase 1 (Arg1), which we demonstrated is potently expressed in pancreatic tumor associated macrophages from both human patients and mouse models. While routinely used as a polarization marker, Arg1 also catabolizes arginine, an amino acid required for T cell activation and proliferation. To investigate this metabolic function, we used a genetic and a pharmacologic approach to target Arg1 in pancreatic cancer. Genetic inactivation of Arg1 in macrophages, using a dual recombinase genetically engineered mouse model of pancreatic cancer, delayed formation of invasive disease, while increasing CD8+ T cell infiltration. Treatment of established tumors with the arginase inhibitor CB-1158 exhibited further increased CD8+ T cell infiltration, beyond that seen with the macrophage-specific knockout, and sensitized the tumors to anti-PD1 immune checkpoint blockade. Thus, our data demonstrate that Arg1 is more than simply a marker of macrophage function. Rather, Arg1 is also a driver of immune suppression and represents a promising immunotherapeutic target for pancreatic cancer.

cancer biology↗

bioRxiv2022

Proteomic identification of the interactome of stalled ribosome nascent chain complexes translating the thylakoid membrane protein D1

The synthesis of multi-span thylakoid membrane proteins initiates at ribosomes off the membrane. Subsequently, the ribosome nascent chain complexes (RNCs) are transferred to the translocase machinery in the thylakoid membrane for cotranslational protein insertion. These steps require finely tuned mechanisms for protein processing, quality control, and targeting to prevent misfolding or aggregation and to ensure efficient transfer of the nascent chain to the insertion machinery. However, little is known about the regulatory network underlying these processes. To identify factors specifically involved in the cotranslational biogenesis of the reaction center protein D1 of photosystem II we established a chloroplast-derived in vitro translation method that allows the production and affinity purification of stalled RNCs bearing nascent chains of D1 of different defined lengths. Stalled RNCs translating the soluble ribosomal subunit uS2c were affinity-purified for comparison. Quantitative tandem-mass spectrometry revealed a set of about 120 proteins specifically associated with D1 RNCs. The interactome includes proteins with broad functions in protein processing, biogenesis and metabolic pathways, such as chlorophyll biosynthesis. We identified STIC2 as a new factor specifically associated with D1 RNCs. Furthermore, our results demonstrated that the interaction of STIC2 with the thylakoid insertase Alb3 and its homologue Alb4 is mediated by the conserved motif III within the C-terminal regions of Alb3 and Alb4. Our data suggest that STIC2 is involved in cotranslational substrate delivery at the thylakoid membrane by coordinating the binding of the D1 RNCs to the insertase machinery.

plant biology↗