The Spike Protein of SARS-CoV-2 Is Adapting Because of Selective Pressures.

The global scale of the COVID-19 pandemic has demonstrated the evolution of SARS-CoV-2 and the clues of adaptation. After two years and two months since the declaration of the pandemic, several variants have emerged and become fixed in the human population thanks to extrinsic selective pressures but also to the inherent mutational capacity of the virus. Here, we applied a neutral substitution evolution test to the spike (S) protein of Omicron's protein and compared it to the others' variant of concern (VOC) neutral evolution. We carried out comparisons among the interactions between the S proteins from the VOCs (Alpha, Beta, Gamma, Delta and Omicron) and the receptor ACE2. The shared amino acids among all the ACE2 binding S proteins remain constant, indicating that these amino acids are essential for the accurate binding to the receptor. The complexes of the RBD for every variant with the receptor were used to identify the amino acids involved in the protein-protein interaction (PPI). The RBD of Omicron establishes 82 contacts, compared to the 74 of the Wuhan original viral protein. Hence, the mean number of contacts per residue is higher, making the contact thermodynamically more stable. The RBDs of the VOCs are similar in sequence and structure; however, Omicron's RBD presents the largest deviation from the structure by 1.11 Å RMSD, caused by a set of mutations near the glycosylation N343. The chemical properties and structure near the glycosylation N343 of the Omicron S protein are different from the original protein, which provoke reduced recognition by the neutralizing antibodies. Our results hint that selective pressures are induced by mass vaccination throughout the world and by the persistence of recurrent infections in immunosuppressed individuals, who did not eliminate the infection and ended up facilitating the selection of viruses whose characteristics are different from the previous VOCs, less pathogenic but with higher transmissibility.

Outcomes of pediatric patients with therapy-related myeloid neoplasms.

Long-term outcomes after allogeneic hematopoietic cell transplantation (HCT) for therapy-related myeloid neoplasms (tMNs) are dismal. There are few multicenter studies defining prognostic factors in pediatric patients with tMNs. We have accumulated the largest cohort of pediatric patients who have undergone HCT for a tMN to perform a multivariate analysis defining factors predictive of long-term survival. Sixty-eight percent of the 401 patients underwent HCT using a myeloablative conditioning (MAC) regimen, but there were no statistically significant differences in the overall survival (OS), event-free survival (EFS), or cumulative incidence of relapse and non-relapse mortality based on the conditioning intensity. Among the recipients of MAC regimens, 38.4% of deaths were from treatment-related causes, especially acute graft versus host disease (GVHD) and end-organ failure, as compared to only 20.9% of deaths in the reduced-intensity conditioning (RIC) cohort. Exposure to total body irradiation (TBI) during conditioning and experiencing grade III/IV acute GVHD was associated with worse OS. In addition, a diagnosis of therapy-related myelodysplastic syndrome and having a structurally complex karyotype at tMN diagnosis were associated with worse EFS. Reduced-toxicity (but not reduced-intensity) regimens might help to decrease relapse while limiting mortality associated with TBI-based HCT conditioning in pediatric patients with tMNs.

Early clinical, histological, and immunohistochemical findings in suspected acute graft-versus-host disease and their association with patient outcomes.

BACKGROUND/OBJECTIVES: Acute graft-versus-host disease (aGVHD) is a serious condition after allogeneic hematopoietic stem cell transplantation (HSCT), frequently involving skin, gut, and liver. It can be difficult to diagnose early, yet this is vital for adequate management. We sought to identify initial clinical and histopathological features in children with suspected GVHD and the association with clinical course and outcomes. METHODS: Retrospective study of patients with skin biopsies for suspected aGVHD from 2006 to 2016. We collected demographic and clinical information, histologic, and immunohistochemical (IHC) findings, and outcomes during follow-up. Bivariate and multivariate analyses were done to identify risk factors associated with remission, development of severe/life-threatening aGVHD, and mortality. RESULTS: We included 42 patients, 15 females. Skin manifestations occurred 51 days (median) after HSCT. On biopsy, 76.2% had mild (stage 1-2) skin aGVHD; during the course of the disease, severity and systemic involvement increased to global grade III/IV in 66.6%. All patients received treatment; 15 are in remission from aGVHD and 23 have died. Histologic features were diagnostic in 83.3%. On bivariate and multivariate analysis, we identified initial clinical and histologic findings that were associated with the measured outcomes: odds of remission from aGVHD were increased when focal vacuolar changes were found on skin biopsy (OR 6.028; 95%CI:1.253-28.992) but decreased by initial hepatic aGVHD (OR 0.112; 95%CI: 0.017-0.748); severe/life-threatening aGVHD was associated with initial gastrointestinal aGVHD (OR 6.054; 95%CI:1.257-29.159); and odds of mortality were decreased with male donor (OR 0.056; 95%CI:0.004-0.804), nulliparous female donor (OR 0.076; 95%CI:0.009-0.669), and focal vacuolar changes on skin biopsy (OR 0.113; 95%CI:0.017-0.770). CONCLUSIONS: We found novel indicators predictive of remission, severity, and mortality in children with aGVHD. Further studies of this condition in children are needed.

FANCC Dutch founder mutation in a Mennonite family from Tamaulipas, México.

BACKGROUND: Fanconi anemia (FA) (OMIM #227650) is a rare hereditary disease characterized by genomic instability. The clinical phenotype involves malformations, bone marrow failure, and cancer predisposition. Genetic heterogeneity is a remarkable feature of FA; at least 22 FANC genes are known to cooperate in a unique FA/BRCA repair pathway. A common rule on the mutations found in these genes is allelic heterogeneity, except for mutations known to have arisen from a founder effect like the FANCC c.67delG in the Dutch Mennonite Community. Here, we present an 11-year-old male patient, member of the Mennonite Community of Tamaulipas México, with a clinical and cytogenetic diagnosis of FA. METHOD: Chromosome fragility test was performed in all siblings. Genomic DNA was obtained from peripheral blood samples. Sanger sequencing was used to identify the FANCC c.67delG mutation (NC_000009.11(NM_000136.2):c.67delG p.(Asp23IlefsTer23)) and its accompanying haplotype. RESULTS: The FANCC c.67delG mutation in 13 members of his family confirmed a FA diagnosis in two of his siblings and identified heterozygous carriers. Haplotype analysis supports that in this family, FA is caused by the founder mutation that initially appeared in Mennonite Dutch and followed this population's migrations through Canada and further to Mexico. CONCLUSION: The identification of the FANCC c.67delG mutation in this family not only allows proper genetic counseling, but it also grants the possibility to raise awareness of FA risk among the Mennonite community living in Mexico.

[Hematopoietic progenitors transplantation in a patient with chronic granulomatous disease in Mexico]. / Trasplante de progenitores hematopoyéticos en un paciente con enfermedad granulomatosa crónica en México.

The incidence of chronic granulomatous disease in international reports is 1:250,000; however, in Mexico it is unknown. At the National Institute of Pediatrics of Mexico a project for facilitating the diagnosis of the disease was implemented by us in 2009. From the start of such project up to date 68 cases have been studied; 80% of those are X-linked forms (LX) and moreover, it has become noticeable the diagnosis at a younger age. The new challenge we are facing its to provide a successful treatment to those patients diagnosed with chronic granulomatous disease (CGD). We are reporting the case of a one-month old newborn patient diagnosed with CGD-LX that was successfully transplanted in Mexico.

La incidencia de la enfermedad granulomatosa crónica en reportes internacionales es de 1:250,000; sin embargo, en México se desconoce. En el Instituto Nacional de Pediatría, a partir de 2009 se implementó un proyecto para facilitar el diagnóstico de esa enfermedad. De esa fecha al día de hoy se han estudiado 68 casos, de los que 80% son formas ligadas al cromosoma X, además de que cada vez los casos se han diagnosticado a una edad más temprana. En la actualidad nos encontramos con un nuevo reto: el tratamiento curativo de los pacientes con enfermedad granulomatosa crónica. Comunicamos el caso de un paciente con enfermedad granulomatosa crónica ligada al cromosoma X, trasplantado exitosamente al mes de vida en México.

Expression of Ik6 and Ik8 Isoforms and Their Association with Relapse and Death in Mexican Children with Acute Lymphoblastic Leukemia.

Expression of the 6 and 8 dominant-negative Ikaros isoforms in pediatric patients with acute lymphoblastic leukemia has been associated with a high risk of relapse and death; due to these isoforms disrupting the differentiation and proliferation of lymphoid cells. The aim of this study was to know the frequency of Ik6 and Ik8 in 113 Mexican ALL-children treated within the National Popular Medical Insurance Program to determine whether there was an association with relapse-free survival, event-free survival and overall survival, and to assess its usefulness in the initial stratification of patients. The expression of these isoforms was analyzed using specific primer sets and nested RT-PCR. The detected transcripts were classified according to the isoforms's sizes reported. A non-expected band of 300 bp from one patient was analyzed by sequencing. Twenty-six patients expressed Ik6 and/or Ik8 and one of them expressed a variant of Ik8 denominated Ik8-deleted. Although the presence of them was not statistically associated with lower relapse free survival (p = 0.432), event free survival (p = 0.667) or overall survival (p = 0.531), inferior overall survival was observed in patients that expressed these isoforms and showed high or standard risk by age and white blood-cell count at diagnosis. Of the 26 patients Ik6+ and/or Ik8+, 14 did not present adverse events; from them 6 were exclusively Ik6+ and/or Ik8+, and 8 were positive for the other Ikaros isoforms (Ik1, Ik2, Ik5, Ik3A, Ik4, Ik4A, Ik7). In the patients studied, the expression of Ik6 and Ik8 did not constitute an independent prognostic factor for relapse or death related to disease; therefore, they could not be used in the initial risk stratification.

Significance of CASP8AP2 and H2AFZ expression in survival and risk of relapse in children with acute lymphoblastic leukemia.

Novel biomarkers for risk refinement and stratification in childhood acute lymphoblastic leukemia (ALL) are needed to optimize treatment results. We studied the expression of CASP8AP2 and H2AFZ associated with relapse and survival in bone marrow samples from newly diagnosed children with ALL. We found: (a) an increased risk for early relapse in those patients with low expression of CASP8AP2 (odds ratio [OR] 3.93, 95% confidence interval [CI] 1.40-11.02, p < 0.05) confirming its usefulness as a predictive risk marker, although H2AFZ did not present the same effect; (b) patients with low expressions of CASP8AP2 and H2AFZ had inferior survival rates (p < 0.001); (c) the predictive values regarding low expressions of H2AFZ and CASP8AP2 and high white blood cell count suggest that these features could help to identify more accurately patients at greater risk of relapse.

Juvenile polyposis of infancy associated with paracentric inversion and deletion of chromosome 10 in a Hispanic patient: a case report.

Juvenile polyposis of infancy is a rare genetic disorder, involving multiple hamartomatous polyps of the gastrointestinal tract, which usually has a very aggressive clinical course and is often fatal. It is characterized by early onset (during the 1st months of life) and by diffuse juvenile polyposis with anemia, recurrent gastrointestinal bleeding, diarrhea, rectal prolapse, intussusception, protein-losing enteropathy, starvation, and malnutrition. There is a hypothesis that mutation of the tumor-suppressor genes BMPR1A and PTEN, located on the long arm of chromosome 10, is associated with the development of this disease. Medical treatment for this disorder is challenging and should be conservative whenever possible. We present the case of a 3-year-old girl with juvenile polyposis of infancy who eventually died from mesenteric artery thrombosis during surgical colectomy. Karyotype of the patient showed a paracentric inversion in 10q and a deletion in 10p. We will briefly comment on some genetic considerations of this disease.