KRAS inhibition activates an actionable CD24 'don't eat me' signal in pancreas cancer.

KRAS G12C inhibitor (G12Ci) has produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the tumor biology of the KRAS G12C allele and possible bypass mechanisms, we developed a novel autochthonous KRAS G12C -driven PDAC model. Compared to the classical KRAS G12D PDAC model, the G12C model exhibit slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRAS G12C tumors produced modest impact despite stimulating a 'hot' tumor immune microenvironment. Immunoprofiling revealed that CD24, a 'do-not-eat-me' signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRAS G12D -driven PDAC. Our study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC. Significance: Lack of faithful preclinical models limits the exploration of resistance mechanisms to KRAS G12C inhibitor in PDAC. We generated an autochthonous KRAS G12C -driven PDAC model, which revealed allele-specific biology of the KRAS G12C during PDAC development. We identified CD24 as an actionable adaptive mechanisms in cancer cells induced upon KRAS G12C inhibition and blocking CD24 sensitizes PDAC to KRAS inhibitors in preclinical models.

Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization.

The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.

Characterisation of the RNA Virome of Nine Ochlerotatus Species in Finland.

RNA viromes of nine commonly encountered Ochlerotatus mosquito species collected around Finland in 2015 and 2017 were studied using next-generation sequencing. Mosquito homogenates were sequenced from 91 pools comprising 16-60 morphologically identified adult females of Oc. cantans, Oc. caspius, Oc. communis, Oc. diantaeus, Oc. excrucians, Oc. hexodontus, Oc. intrudens, Oc. pullatus and Oc. punctor/punctodes. In total 514 viral Reverse dependent RNA polymerase (RdRp) sequences of 159 virus species were recovered, belonging to 25 families or equivalent rank, as follows: Aliusviridae, Aspiviridae, Botybirnavirus, Chrysoviridae, Chuviridae, Endornaviridae, Flaviviridae, Iflaviridae, Negevirus, Partitiviridae, Permutotetraviridae, Phasmaviridae, Phenuiviridae, Picornaviridae, Qinviridae, Quenyavirus, Rhabdoviridae, Sedoreoviridae, Solemoviridae, Spinareoviridae, Togaviridae, Totiviridae, Virgaviridae, Xinmoviridae and Yueviridae. Of these, 147 are tentatively novel viruses. One sequence of Sindbis virus, which causes Pogosta disease in humans, was detected from Oc. communis from Pohjois-Karjala. This study greatly increases the number of mosquito-associated viruses known from Finland and presents the northern-most mosquito-associated viruses in Europe to date.

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation.

The mechanistic understanding of nascent RNAs in transcriptional control remains limited. Here, by a high sensitivity method methylation-inscribed nascent transcripts sequencing (MINT-seq), we characterized the landscapes of N6-methyladenosine (m6A) on nascent RNAs. We uncover heavy but selective m6A deposition on nascent RNAs produced by transcription regulatory elements, including promoter upstream antisense RNAs and enhancer RNAs (eRNAs), which positively correlates with their length, inclusion of m6A motif, and RNA abundances. m6A-eRNAs mark highly active enhancers, where they recruit nuclear m6A reader YTHDC1 to phase separate into liquid-like condensates, in a manner dependent on its C terminus intrinsically disordered region and arginine residues. The m6A-eRNA/YTHDC1 condensate co-mixes with and facilitates the formation of BRD4 coactivator condensate. Consequently, YTHDC1 depletion diminished BRD4 condensate and its recruitment to enhancers, resulting in inhibited enhancer and gene activation. We propose that chemical modifications of eRNAs together with reader proteins play broad roles in enhancer activation and gene transcriptional control.

RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability.

The molecular basis underlying the interaction between retrotransposable elements (RTEs) and the human genome remains poorly understood. Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by developing a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes, and are bound by a dozen RNA binding proteins (RBPs) that are putative novel readers of m6A-modified RNAs, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes with critical roles in DNA damage repair and sometimes in L1 suppression per se, where they act as transcriptional "roadblocks" to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription. Remarkably, our analysis identified thousands of MILs in multiple human fetal tissues, enlisting them as a novel category of cell-type-specific regulatory elements that often compromise transcription of long genes and confer their vulnerability in neurodevelopmental disorders. We propose that this m6A-orchestrated L1-host interaction plays widespread roles in gene regulation, genome integrity, human development and diseases.

Influence of a new monofilament polyester mesh on inflammation and matrix remodeling.

ABSTRACT Synthetic mesh is widely used for hernia repairs, but mesh-induced chronic inflammatory responses may lead to postoperative complications. We previously showed an elevated response to multifilament polyester (PE) versus monofilament polypropylene (PP) and polytetrafluoroethylene (PTFE) meshes, but it is unclear whether this discrepancy is due to the differences in chemical composition or filament structure. This study compares the influence of a newly available monofilament PE mesh to that of multifilament PE, monofilament PP, and monofilament PTFE on the expression of genes important in inflammation and extracellular matrix remodeling in a rat model. Full thickness abdominal wall defects were corrected with onlay repair or suture repair with no mesh. Explants were harvested 7 or 90 days after repair and divided for histology and mRNA analyses using real-time quantitative polymerase chain reaction arrays to profile expression at the tissue-mesh interface. Monofilament PE elicited a reduced foreign body reaction compared to multifilament PE, corresponding with reduced mRNA expression of important inflammatory cytokines and matrix metalloproteinases (MMPs). Unexpectedly, monofilament PE also resulted in markedly reduced mRNA expression of tumor necrosis factor and MMPs 3 and 9 compared to the widely-used monofilament PP mesh. Findings from this study revealed that both chemical composition and filament structure are important mesh characteristics that may affect a patient's wound healing response and clinical outcome, and should be considered by the surgeon when choosing a particular mesh. Although clinical studies are warranted, results in a rodent model suggest that monofilament PE may be more beneficial than the multifilament form for certain hernia repairs.

Inflammatory cytokine and matrix metalloproteinase expression induced by collagen-coated and uncoated polypropylene meshes in a rat model.

OBJECTIVE: The objective of the study was to compare the influence of collagen-coated vs uncoated polypropylene meshes on the expression of genes critical for wound healing. STUDY DESIGN: In 54 rats, abdominal wall defects were created, repaired by polypropylene sutures, and covered by an overlay of coated polypropylene (n = 20), uncoated polypropylene (n = 18), or no mesh (n = 16). Explants were harvested 7 or 90 days after repair and divided for histological, immunohistochemical, and messenger ribonucleic acid (mRNA) analyses. Real-time quantitative polymerase chain reaction arrays were used to profile the expression of 84 genes at the tissue-mesh interface. RESULTS: One week after implantation, coated mesh elicited a slightly greater inflammatory response and increased mRNA expression of 4 proinflammatory cytokines compared with uncoated mesh. Both materials, however, induced a comparable expression of cytokines and matrix metalloproteinases relative to suture repair 90 days after implantation. CONCLUSION: Collagen-coated polypropylene mesh induces elevated inflammatory cytokine expression compared with uncoated mesh early in the healing process, but the response to both meshes is similar 90 days after implantation.

Influence of mesh materials on the expression of mediators involved in wound healing.

The use of synthetic mesh for ventral hernia repair is widely accepted, but mesh-induced inflammatory responses may lead to postoperative complications. Molecular mechanisms that direct the extent of the foreign body reaction to implanted materials are poorly understood. This study compares the influence of three macroporous meshes on the expression of genes critical for wound healing and extracellular matrix remodeling in a rat model. Full thickness abdominal wall defects were corrected with polypropylene, polyester, polytetrafluoroethylene (PTFE), or suture repair with no mesh. Explants were harvested 7 or 90 days after repair and were divided for histological, immunohistochemical, and mRNA analyses. Real-time quantitative polymerase chain reaction arrays were used to profile the expression of 84 genes involved in angiogenesis at the tissue-mesh interface. Evaluation of gene expression profiles and histologic specimens revealed that polypropylene and polyester induced a greater and more persistent inflammatory response than PTFE, which elicited a response most similar to that induced by suture repair. Mesh implantation induced the differential expression (>3-fold change and p < .01) of genes encoding inflammatory cytokines, growth factors, and extracellular matrix proteins relative to suture repair without mesh. Genes most markedly upregulated included the neutrophil chemoattractant CXCL2 and matrix metalloproteinases 3 and 9. Polyester induced the greatest number of differentially expressed genes relative to suture repair both at 7 and 90 days after implantation. Results from this study suggest that the particular type of mesh used in a hernia repair may affect the patient's wound healing response and clinical outcome.