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Chronic neutrophilic leukemia and chronic myelomonocytic leukemia: WHO defined.

The World Health Organization (WHO) classification of myeloid disorders has provided updated parameters for the consistent diagnosis of two previously less than optimally defined chronic myeloid disorders, CNL and CMML. The classification of these disorders, which had been controversial, is now better defined and provides more clinically and biologically relevant disease definitions to enable uniform diagnosis and a framework to evaluate natural history and therapeutic interventions. CNL is now recognized as a distinct entity among the chronic myeloproliferative disorders and CMML is included within the new category of 'myelodysplastic/myeloproliferative diseases' (MDS/MPD). Predominant neutrophilia defines CNL whereas CMML is defined by predominant and monocytosis. In each case these defining features must be distinguished from reactive causes for the same in the absence of clear evidence of myeloid clonality (CNL and CMML) or dysplasia (CMML). The exclusion of underlying bcr/abl-driven oncogenesis is an essential component in the diagnosis of these chronic leukemic processes. The optimal therapy for both CNL and CMML remains uncertain. Current management decisions are based on small studies or extrapolated from therapeutic strategies that are effective in similar chronic, clonal myeloid disorders. Given the potential for evolution to acute leukemia or progressive refractory leucocytosis or cytopenias, allogeneic stem cell transplantation might be appropriate for younger patients. Continued reporting and investigation of specific therapeutic strategies and responses must be encouraged.

Humans↗

Systematic changes in gene expression patterns following adaptive evolution in yeast.

Culturing a population of Saccharomyces cerevisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after continuous aerobic growth in glucose-limited chemostats for more than 250 generations. DNA microarrays were used to compare genome-wide patterns of gene expression in the evolved strains and the parental strain. Several hundred genes were found to have significantly altered expression in the evolved strains. Many of these genes showed similar alterations in their expression in all three evolved strains. Genes with altered expression in the three evolved strains included genes involved in glycolysis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolite transport. These results are consistent with physiological observations and indicate that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.

Adaptation, Physiological↗

T cell repertoire in patients with stable scleroderma.

At onset of systemic sclerosis (SSc), T cells have been found to oligoclonally expand in the skin, presumably in response to auto-antigens, but the T cell repertoire has not been evaluated at a later stage. To determine whether a perpetuating immune response contributes to the pathogenesis of stable SSc, the T cell repertoire was analysed in patients with diffuse (d) or limited (l) SSc, and compared to patients with primary Raynaud's phenomenon (RP) or healthy volunteers (Ctrl). The T cell repertoire (total, CD4 or CD8 sorted blood T cells) was analysed by qualitative and quantitative immunoscope (14 BV families analysed) in 11 untreated dSSc and 11 untreated lSSc, 10 RP and 11 Ctrl. To better detect in vivo activated cells, repertoire analysis was also performed on sorted CD4 T cells after in vitro culture with IL-2. In parallel, 6 skin biopsies from SSc patients were analysed. After 7-8 years of disease evolution, SSc patients did not show detectable clonal T cell expansions in the skin, even after tentative expansion from the biopsy with IL-2. Total T cell, sorted CD4 and CD8 T cell repertoires from the blood of patients with SSc did not show significant perturbation as compared to patients with RP and Ctrl. After IL-2 culture for 7 days, blood CD4 T cells from the patients did not preferentially expand as compared to RP and Ctrl. These findings suggest that antigen-driven immune responses may play a lesser role in established SSc than at disease onset.

CD4-Positive T-Lymphocytes↗

Molecular methods for typing of Helicobacter pylori and their applications.

Microbial typing is a useful tool in clinical epidemiology for defining the source and route of infection, for studying the persistence and reinfection rates, clonal selection in the host and bacterial evolution. Phenotypic methods such as biotyping, serotyping and hemagglutinin typing have little discriminatory power compared to genotypic methods concerning the typing of Helicobacter pylori. Therefore great efforts have been made to establish useful molecular typing methods. In this context, the most frequently used genotypic methods are described based on our own experience and the literature: (1) restriction endonuclease analysis, (2) endonuclease analysis using pulsed-field gel electrophoresis, (3) ribotyping, (4) polymerase chain reaction (using either random primers or repetitive DNA sequence primers), and (5) polymerase chain reaction-restriction fragment length polymorphism analysis of e.g. the urease genes. Furthermore, reproducibility, discriminatory power, ease of performance and interpretation, cost and toxic procedures of each method are assessed. To date no direct comparison of all the molecular typing methods described has been performed in the same study with the same H. pylori strains. However, PCR analysis of the urease gene directly on suspensions of H. pylori or gastric biopsy material seems to be useful for routine use and applicable in specific epidemiological situations.

Bacterial Typing Techniques↗

Aplastic anemia: management of adult patients.

The primary therapeutic approach to acquired aplastic anemia (AA) in older adults differs from the primary approach used in children and younger adults because in the former group, the results of allogeneic bone marrow transplantation (BMT) are less favorable. With increasing age of the patients, immunosuppressive therapy with antithymocyte globulin (ATG) and cyclosporine (CsA) constitutes the primary treatment option and may be better than BMT. There are very few clinical clues as to the selection of patients likely to respond to immunosuppression. Repeated ATG/CsA cycles are often used as salvage regimens, but in refractory patients BMT may be the best treatment option, as the prognosis for non-responders is poor without definitive treatment. Conservative therapy such as intense immunosuppression is associated with a high relapse rate but does not impact the survival and overall prognosis. The inability to eliminate autoimmune T cell clones using current therapeutic strategies suggests that prolonged immunosuppressive maintenance therapy may be needed for a substantial proportion of patients. Late clonal complications of conservatively treated patients include evolution to myelodysplasia and paroxysmal nocturnal hemoglobinuria and may develop in 20% of the patients. However, BMT also has several sequelae including an increased frequency of solid tumors. Novel immunosuppressive and immunomodulatory agents and constantly improving results of allogeneic BMT will further improve the survival rate of adult patients with AA.

Adolescent↗

Balancing photosynthetic light-harvesting and light-utilization capacities in potato leaf tissue during acclimation to different growth temperatures.

We investigated the effect of temperature during growth and development on the relationship between light-harvesting capacity, indicated by chlorophyll concentration, and light-utilization potential, indicated by light- and bicarbonate-saturated photosynthetic oxygen evolution, in Solanum tuberosum L. cv. Norland. Clonal plantlets were transplanted and grown at 20 degrees C for 2 weeks before transfer to 12, 16, 20, 24 and 28 degrees C for 6 weeks. After 4 weeks of the temperature treatments, leaf tissue fresh weights per area were one-third higher in plants grown at 12 degrees C vs those grown at 28 degrees C. Conversely, chlorophyll content per area in tissue grown at 12 degrees C was less than one-half of that of tissue grown at 28 degrees C at 4 weeks. Photosynthetic capacity measured at a common temperature of 20 degrees C and expressed on a chlorophyll basis was inversely proportional to growth temperature. Leaf tissue from plants grown at 12 degrees C for 4 weeks had photosynthetic rates that were 3-fold higher on a chlorophyll basis than comparable tissue from plants grown at 28 degrees C. These results suggest that the relationship between light-harvesting capacity and light-utilization potential varies 3-fold in response to the growth temperatures examined. The role of this response in avoidance of photoinhibition is discussed.

Acclimatization↗

Cellular and molecular mechanisms of carcinogenesis in lining epithelia.

Lining epithelia are the major target sites for cancer in man. The induction of carcinomas on mouse skin following the application of chemical agents is the prototype model for cancer development in a lining epithelium. In this tissue, the earliest carcinogen-induced lesion, initiation, results in an epidermal cell with an altered program of terminal differentiation. Such "initiated" cells can be selected in culture since normal cells can be induced to terminally differentiate by Ca2+ or phorbol ester tumor promoters and will be lost from the cultured population. In situ, the growth of initiated cells is suppressed by surrounding normal cells. The differentiation-inducing effects of tumor promoters on normal cells, therefore, are essential in providing a selective growth advantage which results in the clonal selection of initiated cells and the evolution of a papilloma. This benign tumor is the pathological manifestation of the initiated phenotype. The c-rasH gene appears to be one target for initiating carcinogens, as a mutated and activated form of this gene is frequently isolated from chemically induced papillomas. Furthermore, the introduction of an activated rasH gene into cultured normal keratinocytes produces papillomas when the cells are transplanted as a skin graft in vivo. After a long latency period, some papillomas convert to carcinomas. Since the conversion process can be accelerated and the frequency enhanced by mutagens, it is presumed that genetic damage in papilloma cells plays an important role in malignant conversion. In papilloma cells lacking an activated rasH oncogene, introduction of an exogenous rasH oncogene leads to malignant progression. Thus, mutation and activation of this gene can contribute to early or late events in skin carcinogenesis. In either case it appears that the rasH oncogene must cooperate with other genetic changes to contribute to the malignant phenotype.

Animals↗

Evolution: setting the mutation rate.

A recent study of X-chromosome and autosome genes in mammals suggests that selective trade-offs are important in the long-term evolution of mutation rates; but recent studies with bacteria show that high mutation rates can nonetheless evolve in the short term in clonal populations.

Animals↗

Stochastic cancer progression driven by non-clonal chromosome aberrations.

Cancer research has previously focused on the identification of specific genes and pathways responsible for cancer initiation and progression based on the prevailing viewpoint that cancer is caused by a stepwise accumulation of genetic aberrations. This viewpoint, however, is not consistent with the clinical finding that tumors display high levels of genetic heterogeneity and distinctive karyotypes. We show that chromosomal instability primarily generates stochastic karyotypic changes leading to the random progression of cancer. This was accomplished by tracing karyotypic patterns of individual cells that contained either defective genes responsible for genome integrity or were challenged by onco-proteins or carcinogens that destabilized the genome. Analysis included the tracing of patterns of karyotypic evolution during different stages of cellular immortalization. This study revealed that non-clonal chromosomal aberrations (NCCAs) (both aneuploidy and structural aberrations) and not recurrent clonal chromosomal aberrations (CCAs) are directly linked to genomic instability and karyotypic evolution. Discovery of "transitional CCAs" during in vitro immortalization clearly demonstrates that karyotypic evolution in solid tumors is not a continuous process. NCCAs and their dynamic interplay with CCAs create infinite genomic combinations leading to clonal diversity necessary for cancer cell evolution. The karyotypic chaos observed within the cell crisis stage prior to establishment of the immortalization further supports the ultimate importance of genetic aberrations at the karyotypic or genome level. Therefore, genomic instability generated NCCAs are a key driving force in cancer progression. The dynamic relationship between NCCAs and CCAs provides a mechanism underlying chromosomal based cancer evolution and could have broad clinical applications.

Animals↗

Meiosis and sex: potent weapons in the competition between early eukaryotes and prokaryotes.

The earliest eukaryote species almost certainly evolved in an environment dominated by numerous prokaryotic species. If the first eukaryotic cells were larger and grew more slowly than their prokaryotic neighbours, they might well have been at a competitive disadvantage. It is proposed here that the early evolution of meiosis, with its capacity for generating new favourable gene combinations, might have served to offset any such competitive disadvantages. Meiosis and sex could have arisen in an asexually reproducing species and formed a clonal population.

Animals↗

Impermanence of bacterial clones.

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.

Clone Cells↗

[E. coli: resistance to quinolones and beta-lactams of clinical strains isolated in the Franche-Comté region of France].

AIM OF THE STUDY: Numerous European studies have reported an increase of resistance to quinolones among E. coli. We conducted a regional study to update our knowledge on this evolution. MATERIALS AND METHODS: We evaluated the resistance phenotype and genotype of 115 clinical strains of E. coli. We collected data on individual treatment with fluoroquinolones, and the evolution of the use of these antimicrobial agents. RESULTS: Resistance to nalidixic acid and ciprofloxacin was 13.0 and 6.9, respectively. The frequency of resistance increased from 1999 to 2001, from 7.5% to 13.0% for nalidixic acid and from 5.4% to 6.9% for fluoroquinolones. Resistance to quinolones was significantly associated to beta-lactams resistance and was slightly higher for nosocomial isolates compared to community-acquired isolates. Previous treatment with fluoroquinolones was the major risk factor associated to E. coli resistance. From 1997 to 2001, fluoroquinolones use has increased in our hospital and particularly in the community. Analysis of molecular epidemiology shows a large clonal diversity among E. coli isolates. CONCLUSION: This study confirms the evolution through resistance to quinolones of E. coli isolates. This observation is not due to dissemination of resistant clonal strains and the selective pressure exerted by fluoroquinolones influences this evolution. Therapeutic alternatives, surveillance, and restriction of fluoroquinolones use are needed to control this spread of resistance.

Adult↗

Serial phenotypic, cytogenetic and molecular genetic studies in Richter's syndrome: demonstration of lymphoma development from the chronic lymphocytic leukaemia cells.

In this report we describe a unique longitudinal study on the clinical, phenotypic, cytogenetic and molecular genetic features of malignant cells from diagnosis of chronic lymphocytic leukaemia (CLL) to the development of lymphoma and lymphomatous meningitis. CLL cells at diagnosis were CD5+, CD19+, surface IgG+, kappa+, were karyotypically abnormal and showed clonal rearrangements in the immunoglobulin heavy (IgH) and kappa light chain genes. Phenotypically leukaemic cells and lymphoma cells at RS resembled CLL at diagnosis, but showed cytogenetic evolution. Geometrically leukaemic cells and lymphoma cells retained the initial clonal rearrangements in IGH and kappa genes, but showed additional supervening clonal rearrangements in both of these genes as the disease progressed to RS. Furthermore, the c-lambda DNA showed clonal rearrangements in the leukaemic cells and lymphoma cells at RS. This complete phenotypic and genotypic analysis of tumour cells during the course of the disease demonstrates the origin of lymphoma from CLL cells through progressive cytogenetic and molecular genetic changes in CLL cells.

Blotting, Southern↗

Differential apoptosis and Fas expression on GPI-negative and GPI-positive stem cells: a mechanism for the evolution of paroxysmal nocturnal haemoglobinuria.

Paroxysmal nocturnal haemoglobinuria (PNH) has a dual pathogenesis. PIG-A mutations generate clones of haemopoietic stem cells (HSC) lacking glycosylphosphatidylinositol (GPI)-anchored proteins and, secondly, these clones expand because of a selective advantage related to bone marrow failure. The first aspect has been elucidated in detail, but the mechanisms leading to clonal expansion are not well understood. We have previously shown that apoptosis and Fas expression in HSC play a role in bone marrow failure during aplastic anaemia. We have now investigated apoptosis in PNH. Ten patients were studied. Apoptosis, measured by flow cytometry, was significantly higher among CD34+ cells from patients compared with healthy controls. Fas expression was also increased. Cells that were stained for CD34, CD59 and apoptosis showed a significantly lower apoptosis in CD34+/CD59- compared with CD34+/CD59+ cells from the same patient. In three patients, staining for CD34, CD59 and Fas revealed lower Fas expression on CD34+/CD59- cells. Differential apoptosis of CD34+/CD59- HSC may be sufficient in itself to explain the expansion of PNH clones in the context of aplastic anaemia. In addition to demonstrating a basic mechanism underlying PNH clonal expansion, these results suggest further hypotheses for the evolution of PNH, based on the direct or indirect resistance of GPI-negative HSC to pro-inflammatory cytokines.

Adolescent↗

Molecular evolution of chronic myeloid leukaemia.

Chronic myeloid leukaemia (CML) is a clonal disorder of the pluripotent haematopoietic stem cell. The typical triphasic course of CML starts with the premalignant chronic phase initiated by BCR-ABL hybrid oncogene formation. Secondary genetic and epigenetic aberrations accompany the progression to the accelerated phase and fatal blastic crisis. Properly timed bone marrow transplantation in eligible patients can result in durable remissions or cure. Both of these states are often accompanied by a long-term persistence of quiescent leukaemic cells. Accordingly, a "functional cure" (i.e. tumour dormancy induction), rather than complete eradication of the malignant cells, is an adequate therapeutical goal. The level of the residual BCR-ABL-positive clones should be monitored and salvage treatment initiated whenever these quiescent leukaemic cells exit their dormant state.

Evolution, Molecular↗

Clonal variation and covariation in aphid resistance to parasitoids and a pathogen.

The potential rate of evolution of resistance to natural enemies depends on the genetic variation present in the population and any trade-offs between resistance and other components of fitness. We measured clonal variation and covariation in pea aphids (Acyrthosiphon pisum) for resistance to two parasitoid species (Aphidius ervi and A. eadyi) and a fungal pathogen (Erynia neoaphidis). We found significant clonal variation in resistance to all three natural enemies. We tested the hypothesis that there might be trade-offs (negative covariation) in defensive ability against different natural enemies, but found no evidence for this. All correlations in defensive ability were positive, that between the two parasitoid species significantly so. Defensive ability was not correlated with fecundity. A number of aphid clones were completely resistant to one parasitoid (A. eadyi), but a subset of these failed to reproduce subsequently. We discuss the factors that might maintain clonal variation in natural enemy resistance.

Animals↗

Beyond Morphology: Reframing Lymph-Node Metastasis Prediction Through Clonal Ecology-Decades-Long Genomic Instability and Polyclonal-to-Monoclonal Transitions as the Missing Dimension in Cancer.

Recent whole-genome, lineage-tracing, single-cell, and spatial studies have reshaped our understanding of tumor evolution, revealing that cancers can arise from polyclonal populations, undergo decades-long genomic instability before clinical detection, and progress through dynamic changes in subclonal composition, cellular state, and ecological organization. These findings challenge the assumption underlying morphology-based prediction models that metastatic risk can be inferred from static histological features alone. Here, we revisit lymph-node metastasis prediction in colorectal cancer through clonal ecology, integrating computational pathology with evolutionary oncology. Drawing on the subclonal switchboard model proposed in 2012 and subsequent artificial intelligence (AI)-enabled approaches for tracking dominant and dormant subclones, we synthesize evidence that metastatic potential reflects clonal ancestry, evolutionary timing, spatial niche architecture, cellular plasticity, intercellular interactions, dormancy, and treatment-driven shifts in subclonal fitness. We define five complementary methodological pillars for operationalizing clonal ecology: single-cell transcriptomics for resolving rare subclones, evolutionary trajectories, and adaptive cell states; lineage tracing and phylogenetics for reconstructing clonal ancestry and divergence; spatial transcriptomics and genomics for mapping subclonal geography and tumor-stromal-immune interactions; longitudinal liquid biopsy surveillance for monitoring residual disease, clonal turnover, and emerging resistance; and AI-enabled multimodal integration for connecting histopathology, genomics, spatial biology, and longitudinal data into predictive ecological-state models. Multiple-instance learning and pathology foundation models provide scalable computational foundations for evolution-aware prediction. Translationally, dormant subclones represent actionable reservoirs of recurrence. A longitudinal clinical and experimental study of KMT2A-rearranged acute myeloid leukemia further supports central predictions of the subclonal switchboard framework by demonstrating treatment-associated shifts in subclonal dominance, persistence of cryptic adaptive programs, and ecological rewiring during resistance and relapse. We propose clonal ecology as a measurable dimension for extending morphology-driven prediction toward integrative models that anticipate evolutionary transitions, identify therapeutic windows, and proactively constrain adaptive tumor ecosystems before resistant or metastatic subclones achieve clinical dominance.

Humans↗

Helicobacter pylori eradication for the treatment of low-grade gastric MALT lymphoma: follow-up together with sequential molecular studies.

BACKGROUND: Helicobacter pylori infection is associated with low-grade gastric MALT lymphoma, and available data support that the eradication of the H. pylori can cause histological regression of the lymphoma. PATIENTS AND METHODS: Nine patients with low-grade gastric MALT lymphoma were treated with amoxicillin, metronidazole, and omeprazole for 14 days in a prospective study. Patients were followed up with sequential endoscopy, mapping gastric biopsies, and molecular studies with PCR amplification of the IgH gene in order to assess the response to H. pylori eradication and the evolution of the histological molecular responses. RESULTS: H. pylori was eradicated in all patients and reinfections were not demonstrated. After H. pylori eradication treatment, the lymphoma regressed both endoscopically and histologically in eight of the nine patients (88.8%). In four of the eight histologically cured patients, no clonal band was detected by PCR; in the remaining four patients; PCR identified a clonal band, which disappeared in all patients after a mean of 12 +/- 4 months. No clonal band was detected by the PCR analysis in any of the eight patients with histological regression after a median of 7 +/- 6 months (range 1-20). The seven followed-up patients have a persistent clinical and histological remission after a median of 14 +/- 5 months. CONCLUSIONS: (1) Low-grade gastric MALT lymphoma can be histologically cured with eradication therapy for H. pylori. (2) After histological regression, PCR amplification of the IgH gene can identify an eventually persisting clonal population. (3) Sequential histological and molecular studies are essential for the assessment of the evolution of the lymphoma. (4) The clonal population tends to disappear, but its disappearance may be delayed for months. (5) Patients with histological regression but with a persistent clonal band should not be treated unless the lymphoma can be histologically demonstrated. All these observations suggest that gastric lymphoma can be effectively cured, but the ultimate fate of these patients is unknown until long-term follow-up studies are available.

Aged↗