Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies

Cancer therapy shapes the fitness landscape of clonal hematopoiesis.

Acquired mutations are pervasive across normal tissues. However, understanding of the processes that drive transformation of certain clones to cancer is limited. Here we study this phenomenon in the context of clonal hematopoiesis (CH) and the development of therapy-related myeloid neoplasms (tMNs). We find that mutations are selected differentially based on exposures. Mutations in ASXL1 are enriched in current or former smokers, whereas cancer therapy with radiation, platinum and topoisomerase II inhibitors preferentially selects for mutations in DNA damage response genes (TP53, PPM1D, CHEK2). Sequential sampling provides definitive evidence that DNA damage response clones outcompete other clones when exposed to certain therapies. Among cases in which CH was previously detected, the CH mutation was present at tMN diagnosis. We identify the molecular characteristics of CH that increase risk of tMN. The increasing implementation of clinical sequencing at diagnosis provides an opportunity to identify patients at risk of tMN for prevention strategies

Cell-free DNA from nail clippings as source of normal control for genomic studies in hematologic malignancies

Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patient management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs. In contrast to solid tumors, conventional sources of normal control (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we find nail cfDNA is a robust source of germline control for paired genomic studies. In a subset of patients, nail DNA may have tumor DNA contamination, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1482) compared to lymphoid diseases (5.4%; 61/1128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. For nails collected after allogeneic stem-cell transplantation, donor DNA was identified in 22% (11/50). In this cohort, an association with recent history of graft-vs-host disease was identified. These findings should be considered as a potential limitation for the use of nail as normal control but could also provide important diagnostic information regarding the disease process

Clonal hematopoiesis is associated with risk of severe Covid-19.

Acquired somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis or CH) are associated with advanced age, increased risk of cardiovascular and malignant diseases, and decreased overall survival. These adverse sequelae may be mediated by altered inflammatory profiles observed in patients with CH. A pro-inflammatory immunologic profile is also associated with worse outcomes of certain infections, including SARS-CoV-2 and its associated disease Covid-19. Whether CH predisposes to severe Covid-19 or other infections is unknown. Among 525 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we show that CH is associated with severe Covid-19 outcomes (OR = 1.85, 95%=1.15-2.99, p = 0.01), in particular CH characterized by non-cancer driver mutations (OR = 2.01, 95% CI = 1.15-3.50, p = 0.01). We further explore the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH is significantly associated with risk of Clostridium Difficile (HR = 2.01, 95% CI: 1.22-3.30, p = 6×10-3) and Streptococcus/Enterococcus infections (HR = 1.56, 95% CI = 1.15-2.13, p = 5×10-3). These findings suggest a relationship between CH and risk of severe infections that warrants further investigation

Human Metapneumovirus Infection Induces Significant Changes in Small Noncoding RNA Expression in Airway Epithelial Cells

Small noncoding RNAs (sncRNAs), such as microRNAs (miRNA), virus-derived sncRNAs, and more recently identified tRNA-derived RNA fragments, are critical to posttranscriptional control of genes. Upon viral infection, host cells alter their sncRNA expression as a defense mechanism, while viruses can circumvent host defenses and promote their own propagation by affecting host cellular sncRNA expression or by expressing viral sncRNAs. Therefore, characterizing sncRNA profiles in response to viral infection is an important tool for understanding host–virus interaction, and for antiviral strategy development. Human metapneumovirus (hMPV), a recently identified pathogen, is a major cause of lower respiratory tract infections in infants and children. To investigate whether sncRNAs play a role in hMPV infection, we analyzed the changes in sncRNA profiles of airway epithelial cells in response to hMPV infection using ultrahigh-throughput sequencing. Of the cloned sncRNAs, miRNA was dominant in A549 cells, with the percentage of miRNA increasing in a time-dependent manner after the infection. In addition, several hMPV-derived sncRNAs and corresponding ribonucleases for their biogenesis were identified. hMPV M2-2 protein was revealed to be a key viral protein regulating miRNA expression. In summary, this study revealed several novel aspects of hMPV-mediated sncRNA expression, providing a new perspective on hMPV–host interactions

script

A Python script to construct FASTA files containing reconstructed genome sequences of evolved clones after DNA rearrangements

Scanning the Landscape of Genome Architecture of Non-O1 and Non-O139 <i>Vibrio cholerae</i> by Whole Genome Mapping Reveals Extensive Population Genetic Diversity

<div><p>Historically, cholera outbreaks have been linked to <i>V</i>. <i>cholerae</i> O1 serogroup strains or its derivatives of the O37 and O139 serogroups. A genomic study on the 2010 Haiti cholera outbreak strains highlighted the putative role of non O1/non-O139 <i>V</i>. <i>cholerae</i> in causing cholera and the lack of genomic sequences of such strains from around the world. Here we address these gaps by scanning a global collection of <i>V</i>. <i>cholerae</i> strains as a first step towards understanding the population genetic diversity and epidemic potential of non O1/non-O139 strains. Whole Genome Mapping (Optical Mapping) based bar coding produces a high resolution, ordered restriction map, depicting a complete view of the unique chromosomal architecture of an organism. To assess the genomic diversity of non-O1/non-O139 <i>V</i>. <i>cholerae</i>, we applied a Whole Genome Mapping strategy on a well-defined and geographically and temporally diverse strain collection, the Sakazaki serogroup type strains. Whole Genome Map data on 91 of the 206 serogroup type strains support the hypothesis that <i>V</i>. <i>cholerae</i> has an unprecedented genetic and genomic structural diversity. Interestingly, we discovered chromosomal fusions in two unusual strains that possess a single chromosome instead of the two chromosomes usually found in <i>V</i>. <i>cholerae</i>. We also found pervasive chromosomal rearrangements such as duplications and indels in many strains. The majority of <i>Vibrio</i> genome sequences currently in public databases are unfinished draft sequences. The Whole Genome Mapping approach presented here enables rapid screening of large strain collections to capture genomic complexities that would not have been otherwise revealed by unfinished draft genome sequencing and thus aids in assembling and finishing draft sequences of complex genomes. Furthermore, Whole Genome Mapping allows for prediction of novel <i>V</i>. <i>cholerae</i> non-O1/non-O139 strains that may have the potential to cause future cholera outbreaks.</p></div

UPGMA method based dendrograms of Sakazaki serogroup strains.

<p>Whole Genome Mapping data based distance matrix with default parameters was used to generate the dendrograms. The three clusters (epidemic <i>V</i>. <i>cholerae</i> Classical and El Tor, one group of environmental isolates from rat, and <i>V</i>. <i>mimicus</i>) are indicated on the branches. The distribution of VPI and CTX on chromosome I in non-O1/non-O139 strains are indicated as well. The different colors of the highlighted strains indicate the following characteristics: No highlight- Clinical; Gray-environmental; Light green (serogroups O2-O4) source unknown; Yellow: epidemic O1 Classical and El Tor; Green: non-O1 epidemic strains; Pink: <i>V</i>. <i>mimicus</i>; Blue: One <i>V</i>. <i>mimicus</i> isolate (serogroup O115) that has the VPI cluster; Orange: Clinical and carry both VPI and CTX clusters; Light red (O77, O49, O80, O53): Clinical and carry VPI only. Scale: 0.2 = 20% dissimilarity.</p

Whole Genome Mapping using different restriction enzymes supports the Chr I and Chr II fusions in <i>V</i>. <i>cholerae</i> 1154–74 (O49) and 10432–62 (O27) strains.

<p>A) The top four panels of maps are derived from strain 1154–74 (O49) and B) the bottom 3 panels are from strain 10432–61 (O27). In each panel, the top and bottom maps indicate <i>in silico</i> generated Chr II and Chr I restriction maps of M66–2 sequences respectively, compared to the experimentally generated maps (middle) of 1154–74 or 10432–62 using indicated restriction enzymes. The fusion in 1154–74 (O49) is around 1.29 Mb of Chr I (size 2.89 Mb) to 0.32 Mb of Chr II (size 1.05) of M66–2. The fusion in 10432–62 (O27) has occurred around 2.80 Mb of Chr I (2.89 Mb) to around 0.83 Mb of Chr II (1.05 Mb) in M66–2. The blue region indicates a single copy match between the chromosomes compared.</p

Whole Genome Maps using different restriction enzymes show putative tandem duplication of chromosomal regions.

<p>A: Top four panels of maps generated using <i>Bam</i>HI, <i>Nhe</i>I, <i>Kpn</i>I and <i>Afl</i>III respectively show the duplicated region in <i>V</i>. <i>cholerae</i> 1154–74 (O49). B: The bottom three panels of maps are that of 10432–62 (O27) using <i>Bam</i>HI, <i>Nhe</i>I and <i>Afl</i>III. In both cases, the location of duplication was found to be around 1240 kb to 1506 kb on reference M66–2 Chr I. The duplicated genome segments are indicated by the orange box in the <i>in silico</i> map of the reference strain. In some panels both assemblies with the single and two copies (resulting from re-analyses of the single molecule data from this region) are shown. The duplicated copies where they could be resolved are indicated by the red circles. The exact lengths of the duplications in the two strains cannot be unequivocally determined by this WGM data. It is also possible that the maps represent a mixed population of cells containing single and two copies of the duplication. (Scale bar 100 Kb).</p