Over the past 25 years, the powerful combination of genome sequencing and bioinformatics analysis has played a crucial role in interpreting information encoded in bacterial genomes. High-throughput sequencing technologies have paved the way towards understanding an increasingly wide range of biological questions. This revolution has enabled advances in areas ranging from genome composition to how proteins interact with nucleic acids. This has created unprecedented opportunities through the integration of genomic data into clinics for the diagnosis of genetic traits associated with disease. Since then, these technologies have continued to evolve, and recently, long-read sequencing has overcome previous limitations in terms of accuracy, thus expanding its applications in genomics, transcriptomics and metagenomics. In this review, we describe a brief history of the bacterial genome sequencing revolution and its application in public health and molecular epidemiology. We present a chronology that encompasses the various technological developments: whole-genome shotgun sequencing, high-throughput sequencing, long-read sequencing. We mainly discuss the application of next-generation sequencing to decipher bacterial genomes. Secondly, we highlight how long-read sequencing technologies go beyond the limitations of traditional short-read sequencing. We intend to provide a description of the guiding principles of the 3rd generation sequencing applications and ongoing improvements in the field of microbial medical research.

Although senescent cells can be eliminated by the immune system, they tend to accumulate with age in various tissues. Here we show that senescent cells can evade immune clearance by natural killer (NK) cells by upregulating the expression of the disialylated ganglioside GD3 at their surface. The increased level of GD3 expression on senescent cells that naturally occurs upon aging in liver, lung, kidney or bones leads to a strong suppression of NK-cell-mediated immunosurveillance. In mice, we found that targeting GD3⁺ senescent cells with anti-GD3 immunotherapy attenuated the development of experimentally induced or age-related lung and liver fibrosis and age-related bone remodeling. These results demonstrate that GD3 upregulation confers immune privilege to senescent cells. We propose that GD3 acts as a senescence immune checkpoint (SIC) that allows senescent cells to escape immunosurveillance and to trigger immune anergy during aging.

Cellular senescence triggers various types of heterochromatin remodeling that contribute to aging. However, the age-related mechanisms that lead to these epigenetic alterations remain elusive. Here, we asked how two key aging hallmarks, telomere shortening and constitutive heterochromatin loss, are mechanistically connected during senescence. We show that, at the onset of senescence, pericentromeric heterochromatin is specifically dismantled consisting of chromatin decondensation, accumulation of DNA breakages, illegitimate recombination and loss of DNA. This process is caused by telomere shortening or genotoxic stress by a sequence of events starting from TP53-dependent downregulation of the telomere protective protein TRF2. The resulting loss of TRF2 at pericentromeres triggers DNA breaks activating ATM, which in turn leads to heterochromatin decondensation by releasing KAP1 and Lamin B1, recombination and satellite DNA excision found in the cytosol associated with cGAS. This TP53–TRF2 axis activates the interferon response and the formation of chromosome rearrangements when the cells escape the senescent growth arrest. Overall, these results reveal the role of TP53 as pericentromeric disassembler and define the basic principles of how a TP53-dependent senescence inducer hierarchically leads to selective pericentromeric dismantling through the downregulation of TRF2.

Homeostatic renal filtration relies on the integrity of podocytes, which function in glomerular filtration. These highly specialized cells are damaged in 90% of chronic kidney disease, representing the leading cause of end-stage renal failure. Although modest podocyte renewal has been documented in adult mice, the mechanisms regulating this process remain largely unknown and controversial. Using a mouse model of Adriamycin-induced nephropathy, we find that the recovery of filtration function requires up-regulation of the endogenous telomerase component TERT. Previous work has shown that transient overexpression of catalytically inactive TERT (i-TERT^ci mouse model) has an unexpected role in triggering dramatic podocyte proliferation and renewal. We therefore used this model to conduct specific and stochastic lineage-tracing strategies in combination with high throughput sequencing methods. These experiments provide evidence that TERT drives the activation and clonal expansion of podocyte progenitor cells. Our findings demonstrate that the adult kidney bears intrinsic regenerative capabilities involving the protein component of telomerase, paving the way for innovative research toward the development of chronic kidney disease therapeutics.

A long-held hypothesis in regeneration proposes that developmental processes are re-deployed during regeneration. To investigate this, we compared embryonic and regeneration gene regulatory networks (GRN) in the sea anemone Nematostella vectensis using transcriptomic time series spanning these two developmental trajectories. Here, we show that regeneration reuses cohorts of the embryonic genes along with a small set of genes whose expression dynamics are specific to regeneration. We identified co-expression modules that are either conserved between embryogenesis and regeneration or specific to regeneration, with the latter linked to cellular mechanisms such as apoptosis, tissue remodeling, and wound healing. Functional assays revealed that apoptosis and cWnt signaling pathways are partially MEK/ERK dependent, have largely distinct downstream targets but converge to coordinate regenerative responses. Collectively, these results indicate that regeneration in N. vectensis represents a partial redeployment and extensive rewiring of the embryonic GRN, reactivating developmental modules through a regeneration-specific network logic.