Altucci, L. | bioRxiv Science

bioRxiv2022

Longitudinal single-cell transcriptomics reveals distinct patterns of recurrence in acute myeloid leukemia

The heterogeneity and evolution of AML blasts can render therapeutic interventions ineffective in a yet poorly understood patient-specific manner. To gain insight into the clonal heterogeneity of diagnosis (Dx) and relapse (Re) pairs, we employed whole-exome sequencing and single-cell RNA-seq to longitudinally profile two t(8;21) (AML1-ETO = RUNX1-RUNX1T1), and four FLT3-ITD AML cases. The single cell RNA data underpinned the tumor heterogeneity amongst patient blasts. The Dx-Re transcriptomes of high risk FLT3-ITD pairs formed a continuum from extensively changed in the absence of significantly mutational changes in AML-associated genes to rather similar Dx-Re pair of an intermediate risk FLT3-ITD. In one high risk FLT3-ITD pair, a pathway switched from an AP-1 regulated network in Dx to mTOR signaling in Re. The distinct AML1-ETO pairs comprise clusters that share genes related to hematopoietic stem cell maintenance and cell migration suggesting that the Re leukemic stem cell-like (LSC-like) cells probably evolved from the Dx LSC-like cells. In summary, our study revealed a continuum from drastic transcriptional changes to extensive similarities between respective Dx-Re pairs that are poorly explained by the well-established model of clonal evolution. Our results suggest alternative and currently unappreciated and unexplored mechanisms leading to therapeutic resistance and AML recurrence.

cancer biology↗

bioRxiv2021

Outer membrane vesicles derived from Klebsiella pneumoniae are a driving force for horizontal gene transfer

Gram-negative bacteria release outer membrane vesicles (OMVs) into the extracellular environment. Recent studies recognized these vesicles as vectors to horizontal gene transfer, however the parameters that mediate OMVs transfer within bacterial communities remain unclear. The present study highlights for the first time the transfer of plasmids containing resistance genes via OMVs derived from Klebsiella pneumoniae (K. pneumoniae). This mechanism confers DNA protection and it is plasmid copy number dependent with a ratio of 3.6 time among high copy-number plasmid (pGR) versus low copy number plasmid (PRM) and the transformation efficiency was 3.6 times greater. Therefore, the DNA amount in the vesicular lumen and the efficacy of horizontal gene transfer was strictly dependent on the identity of the plasmid. Moreover, the role of K. pneumoniae-OMVs in interspecies transfer was described. The transfer ability was not related to the phylogenetic characteristics between the donor and the recipient species. K. pneumoniae-OMVs transferred plasmid to Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Burkholderia cepacia. These findings address the pivotal role of K. pneumoniae-OMVs as vectors for antimicrobial resistance genes spread, contributing to the development of antibiotic resistance in the microbial communities. Author summaryK. pneumoniae is an important opportunistic pathogen that affects several host districts, in particular respiratory and urinary tracts. Hospital-acquired K. pneumoniae infections lead to a 50% mortality rate correlated with rapid acquisition of antibiotic resistance. Currently, the increasing rate of antibiotic resistance among K. pneumoniae isolates is a major concern worldwide. The spread of multidrug-resistant K. pneumoniae strains renders current therapeutic options ineffective. Like all Gram-negative bacteria, K. pneumoniae secretes OMVs. OMVs are spherical structures, with a diameter between 50-250 nm, originating from the outer membrane. OMVs biogenesis allows bacteria to interact with the external environment, increasing bacterial survival under stressful conditions and regulating microbial interactions within bacterial communities. Few evidence recognized OMVs as vectors for horizontal gene transfer, contributing to the spread of resistance. In this scenario, the present study examines the potential role of K. pneumoniae-OMVs in inter- and intra-species diffusion of {beta}-lactam resistance.

microbiology↗

bioRxiv2021

DNA Mutations via Chern-Simons Current

We test the validity of a possible schematization of DNA structure and dynamics based on the Chern-Simons theory, that is a topological field theory mostly considered in the context of effective gravity theories. By means of the expectation value of the Wilson Loop, derived from this analogue gravity approach, we find the point-like curvature of genomic strings in KRAS human gene and COVID-19 sequences, correlating this curvature with the genetic mutations. The point-like curvature profile, obtained by means of the Chern-Simons currents, can be used to infer the position of the given mutations within the genetic string. Generally, mutations take place in the highest Chern-Simons current gradient locations and subsequent mutated sequences appear to have a smoother curvature than the initial ones, in agreement with a free energy minimization argument.

biophysics↗