Intestinal T-cell lymphomas (ITCL) are a group of rare and very aggressive extranodal lymphomas classified into five subtypes. The current literature includes a small number of ITCL series from different countries, often focusing on a single ITCL subtype. In this study, we wanted to depict the complete clinical–pathological profile of a series of patients affected by primary ITCL involving the small bowel, diagnosed and treated at a referral center for celiac disease and lymphomas. Furthermore, we tried to define clinical and histopathological hallmarks of these lymphomas to widen the knowledge on these rare and still partially characterized neoplasms.The gastrointestinal (GI) tract is the most common extranodal site of occurrence of non-Hodgkin lymphomas. Most GI lymphomas are of B-cell lineage, while T-cell lymphomas are less frequent. The aim of our retrospective study was to depict the clinical–pathological profile of a series of patients affected by intestinal T-cell lymphomas (ITCL) and possibly define hallmarks of these neoplasms. A total of 28 patients were included: 17 enteropathy-associated T-cell lymphomas (EATL), 5 monomorphic epitheliotropic T-cell lymphomas (MEITL), 3 indolent T-cell lymphoproliferative disorders of the gastrointestinal tract (ITCLDGT), and 3 intestinal T-cell lymphomas not otherwise specified (ITCL-NOS). Celiac disease (CD) was diagnosed in around 70% of cases. Diagnosis of EATL showed a significant correlation with CD30 expression, whereas MEITL with angiotropism and CD56 positivity. ITCLDGT cases showed plasma cells infiltration. Peripheral lymphocytosis, the absence of a previous diagnosis of CD, an advanced Lugano clinical stage, and the histological subtype ITCL-NOS were significantly associated with worse survival at multivariate analysis. Our findings about the epidemiological, clinical, and histopathological features of ITCL were in line with the current knowledge. Reliable prognostic tools for these neoplasms are still lacking but according to our results lymphocytosis, diagnosis of CD, Lugano clinical stage, and histological subtype should be considered for patient stratification. Extranodal lymphomas account for roughly one-third of all lymphoid malignancies. The gastrointestinal (GI) tract is the most common extranodal site involved in non-Hodgkin lymphomas. Between 20% and 40% of them are represented by primary gastrointestinal (GI) lymphomas as defined by the so-called Dowson’s criteria, i.e., 1) the presence of a bowel lesion, (2) the absence of peripheral lymphadenopathies, and 3) normal white blood cell counts [ the pres normal wAccording to the 2022 5th edition of the World Health Organization (WHO) classification, and the 2022 international consensus classification (ICC), ITCL are classified into five subtypes: enteropathy-associated T-cell lymphoma (EATL), monomorphic epitheliotropic ITCL (MEITL), indolent  T-cell lymphoproliferative disorder/lymphoma of the gastrointestinal tract (ITCLDGT), indolent NK-cell lymphoproliferative disorder of the gastrointestinal tract (iNKLPD), and ITCL not otherwise specified (NOS) ,7,9,10.EATL has the highest incidence among ITCL, is more common in Western countries, and arises in patients in their sixties or seventies. Its name relates to its association with celiac disease (CD) and Human Leucocyte Antigen (HLA)-DQ2 allele homozygosity . EATL inMEITL is rarer than EATL in our latitudes, but it shows a higher incidence in Asian and Hispanic populations. Clinically, MEITL displays many similarities with EATL but the association with CD is historically not recognized. MEITL infiltrate is monomorphic and is made of small to medium-sized round cells with scant cytoplasm, and inconspicuous nucleoli. The tumor infiltrate shows a prominent epitheliotropic pattern but lacks inflammatory background. It is usually CD3+, CD4−/CD8+, CD56+, MATK+, expresses cytotoxic molecules, and often lacks CD5, indicating a possible γδ T-cell derivation. TCRγ is often rearranged, and gains at 9q34.3 as well as STAT5b mutations are frequently observed. The behavior and survival are similar to that of EATL ,15,16,17ITCLDGT is a clonal proliferative disorder of small CD8+ intestinal T lymphocytes that lacks destruction of the bowel mucosa, with a typical lymphoid cell infiltration of the lamina propria with displacement of mucosal glands and epithelium sparing, but may be unresponsive to chemotherapy and progress to a frank aggressive ITCL ,18,19.ITCLDGT is limited to the gastrointestinal tract. Presenting symptoms include abdominal pain, weight loss, and diarrhea with a chronic and relapsing clinical course. Proliferative index is low and patients experience a prolonged survival ,18,20.iNKLPD is a recently described entity, previously considered a reactive process because of its self-regressive lesions. It may also involve gallbladder and vagina and it is characterized by an atypical infiltrate of medium-sized cells with NK/T-cell lymphoma phenotype , but lacking EBV infection ,22,23,24Finally, ITCL-NOS is a basket category used for all the primary ITCL lacking the diagnostic criteria for other ITCL subtypes. It more frequently involves the colon, with a proliferation of cytotoxic TCR-silent lymphocytes, and displays an aggressive clinical behavior ,4,8.The literature currently includes a small number of ITCL series from different countries, often focusing on specific biological or molecular features of a single ITCL subtype ,16,26. TWe collected all the GI lymphomas diagnosed at the center between January 2001 and December 2021 and we therefore included in the present study only the cases with a diagnosis of primary ITCL involving the small bowel. Two patients were previously reported by our group .All patients received a histopathological diagnosis of ITCL, with analysis of one or more histological samples and a complete clinical–radiological assessment including computed tomography (CT) and positron electron tomography (PET) at diagnosis. Histopathological diagnosis of ITCL was made according to the 5th edition of WHO classification of hematopoietic tumors . Two expFor each patient we retrieved a pool of clinical data, i.e., sex, age, laboratory tests—blood cell counts, ß2-microglobulin and LDH-, site of involvement, history of CD, symptoms at presentation, gastrointestinal complications—perforation, hemorrhage, fistula, or obstruction, clinical staging, overall survival, treatment, and outcome.To calculate the overall survival (OS) we considered the time between the initial diagnosis and the death or last follow-up. The median follow-up was 12 moths (IQR 8–17).We used the Lugano staging system for GI lymphomas . This syHistopathological and molecular data were also collected  positivity assessed by EBER-ISH, proliferative index, and presence of TCR rearrangement according to BIOMED-2 protocol).p-value < 0.05 was considered statistically significant. Given the low sample size, it was not possible to statistically compare clinical, histopathological, and molecular variables among lymphoma subtypes. The study was approved in 2014 by the local ethics committee, and all participants provided written informed consent for the publication of anonymized data. The study is reported in accordance to the STROBE recommendations for quality assurance.Statistical analysis was performed using R software . We performed univariate survival analyses for clinical and pathological features through the Kaplan–Meier method, and differences were compared with the log-rank test. For the multivariate survival analysis, a Cox regression model was used. Two-sided Between January 2001 and August 2021, we diagnosed at our center 226 cases of GI lymphoma. B-cell lymphomas accounted for 193 cases, while 33 were T-cell lymphomas, including 28 ITCL, 2 ALCL, 1 ENKTCL, and 2 cases of nodal T-cell lymphomas with secondary intestinal involvement.We collected 28 cases of primary ITCL, including 17 EATL, 5 MEITL, 3 ITCLDGT, and 3 ITCL-NOS. No cases of iNKLPD were found in our lymphoma series. ITCL represented 12% of all GI tract lymphomas followed in the last 20 years at our institution. Clinical features are summarized in Lymph nodes were involved in 20/28 cases (71%), with localization to distant stations in 3 cases only. Spleen and/or liver were involved in up to 18% of patients  while bone marrow was involved in 3/28 cases (10%). Other extraintestinal sites involvement, i.e., lung, pancreas, or bladder, was observed in only three cases. The ITCL was associated with a monoclonal gammopathy of undetermined significance (MGUS) in two cases, and with hepatocellular carcinoma or G1 chondrosarcoma in one patient each. Interestingly, the last patient (diagnosed as ITCLDGT) was also affected by Noonan syndrome. CD was diagnosed in around 70% of our patients  GI complications  were observed in more than one-third of cases (10/28). The clinical stage, according to Lugano clinical staging system, was IV (disseminated) in 40% of cases.LDH was elevated in 25/28 (89%) patients. Nevertheless, no patient showed a marked elevation  of the enzyme. Similarly, β2-microglobulin was elevated in all patients (more than 2500 mcg/L), but above 5500 mcg/L in 11/28 patients only. The blood cell counts are reported in The median overall survival (OS) was 12 months. Only 3/28 patients (10.7%) were still alive at the last follow-up and with partial response (>50% of lesion decrease) to chemotherapy, while the remaining died as a consequence of the lymphoma.We could retrieve information regarding treatment schedules in 19/28 cases. These patients were mainly treated according either to CHOP  for the 68% or CHOEP (CHOP plus etoposide) for the 21% schemes. Only two EATL patients were treated with stem cell transplantation: one of them died after 12 months while the other was alive at the last follow-up. Two patients died before receiving any treatment.We performed univariate survival analysis for clinical and histopathological variables.3/μL) and the absence of CD history were associated with a worse outcome for patients with ITCL. All the other clinical variables taken into account and reported in As shown in the Kaplan–Meier plots in p = 0.34).When evaluating the effect of therapy (CHOP vs. CHOEP) on survival, no statistical difference was found with the log-rank rest  showed that ITCL-NOS had the worst survival probability while ITCLDGT had the best .Finally, multivariate analysis confirmed the role of significant variables at univariate, with the addition of Lugano clinical stage. In detail, a Lugano stage of II or greater was correlated with a worse prognosis for patients with ITCL.EATL was the most frequent ITCL observed in our center (64% of cases) and showed the lower M:F ratio. EATL more frequently displayed a disseminated disease and some clinical peculiarities compared to other ITCL. The most frequently involved site was the distal small intestine, with ileum or jejunum being involved in over half of patients. Most EATL cases  had an associated CD, diagnosed before the occurrence of lymphoma (6/17 cases) or at the same time of the tumor diagnosis (7/17 cases). More in detail, a diagnosis of refractory celiac disease (RCD) was made in 6 out of 17 patients. In the two remaining cases, a clear diagnosis of CD could not be established due to EATL severity leading to death and early work-up termination.Clinically, EATL displayed the highest frequency of B-symptoms and organomegaly. Furthermore, it was the only ITCL type to involve the bone marrow in our series. Consistently, 59% of cases were classified as clinical stage III or IV. All but one patient who displayed GI complications in our ITCL cohort were diagnosed as EATL.The median OS of EATL was 12 months.From a histopathological point of view, diagnosis of EATL was not significantly associated with a specific immunophenotype, cell size, or neoplastic infiltrate’s features such as necrosis. Nevertheless, EATL was generally characterized by a polymorphic proliferation of medium to large-sized cytotoxic T-cells frequently expressing CD3 and CD7, double-negative for CD4 and CD8, and staining for CD30 more in than half of cases (11/17) . VillousCompared to other ITCL, in our cohort, MEITL was slightly more frequent in males and had a median age at diagnosis of 60 years. The lymphoma involved only the small intestine, with multiple localizations in a single case. B-symptoms were observed in 40% of cases, while organomegaly was present in one single patient. Regional lymph node involvement was present in 80% of cases. Interestingly, three of our MEITL patients received a diagnosis of CD. A total of 60% of patients displayed a clinical stage I or II.All patients died within a median of 12 months.+, CD2+, CD7+, and TIA-1+. All patients were positive for CD56 and 80% of them were CD8+. The CD8 seemed to be more typical of this subtype compared to other subtypes of ITCL, in which it was expressed in only one-third of the cases. A median of 55% of cells were positive for Ki67. A single patient was analyzed and tested positive for TCRγ rearrangements as previously described  and B-symptoms were present in all cases. Moreover, all cases showed involvement of locoregional lymph nodes. Nevertheless, the lymphoma showed no organomegaly, involvement of bone marrow, or distant lymph nodes. Two patients received a first diagnosis of EATL and were treated with CHOP without success. The diagnosis of ITCLDGT was made after a review of the biopsies performed at initial presentation, with a diagnostic delay of 2 months for one case and 4 years for the other. All the ITCLDGT patients of our cohort were at stage IV of Lugano and the OS was of 14 months in median. Only one patient was alive at the last follow-up. This subtype showed the best survival probability, when compared to other subtypes, at univariate and multivariate analysis.The lymphoma cells were small to medium-sized and resulted as positive, in all patients, for CD3, CD2, CD7, and TIA1 and negative for ALK, CD56, CD57, granzyme-B, and Perforin. Two cases were CD4−/CD8+ and one CD4+/CD8−. CD5 and βF1 were positive in one case each. Ki67 proliferative index was low (5–15%). No bystander eosinophils, angiotropism, or necrosis was observed. Interestingly, in two out of three ITCLDGT cases, the infiltrate was rich in plasma cells . One of Three patients received a diagnosis of ITCL-NOS, as it was not possible to make an alternative diagnosis according to the 2022 WHO classification criteria. These were two males and one female with a median of 65 years at diagnosis. They had a more distally localized lymphoma, comparing to other categories, and 2/3 patients displayed multiple sites of involvement over the GI tract. They all presented with B-symptoms and with a high serum concentration of β2-microglobulin . They all had lymph node involvement, including distant stations. Two out of three patients presented with a clinical stage IV. All patients died within a median of 5 months, and at univariate and multivariate analysis, the ITCL-NOS showed the worst survival probability.At histopathological examination, two cases displayed infiltrates made by small to medium-sized cells, and just one by large cells. In two cases, the lymphoma cells expressed CD3, CD7, and Granzyme-B. No cases tested positive for CD4, CD20, CD56, or CD57. Interestingly, two patients displayed necrosis and bystander eosinophils, similarly to our EATL cases. ITCL-NOS showed the higher median proliferative index (Ki67), equal to 60% .ITCL with a primary involvement of the small bowel are a group of rare primary extranodal lymphomas possibly arising from innate intraepithelial intestinal resident T-cells. Even though in most cases ITCL behaves as very aggressive neoplasm, the clinical, histopathological, and molecular features as well as the postulated cell-of-origin differ among the various entities. Moreover, the incidence of the different ITCLs highly depends on the geographic area, as a consequence of the higher incidence of CD in Western countries, and the higher incidence of lymphoma of NK (EBV-driven) or γδ T-cell in Asia and Central and South America .The proportions of different ITCL subtypes in our article reflect the Caucasian origin of all our patients. Indeed, our most frequent diagnosis was of EATL, in most cases being associated with CD. The epidemiological, clinical, and histopathological data of all our patients were in line with the current knowledge. EATL develops in the late adulthood with a slight male predominance and presents with persistent GI and B-symptoms. EATL generally involves the distal small intestine (jejunum and ileum) and may be preceded by clinical and histological evidence of RCD. EATL seems to derive from so-called “type A” innate intraepithelial T-cells  carryingCDKN2A (9p loss/9p21 LOH) and mutation in SETD2, STAT5b, or JAK1/JAK3 genes [EATLs frequently harbor cytogenetic alterations with loss of function of K3 genes . They geExtraintestinal localizations are more common compared to other ITCL and involve both lymphatic and non-lymphatic organs. Interestingly, our data show a high incidence of splenic, and especially liver, involvement.Most patients with EATL had a concurrent or previous diagnosis of CD or RCD. This finding is in keeping with other studies, in which a variable association between EATL and CD (between 38 and 100%) was described ,32. We cThe majority of EATL patients received chemotherapy, respectively, with CHOP or CHOEP schemes. Only two EATL patients were treated with stem cell transplant, and one of them was still alive at the last follow-up. Although there are no standardized treatment protocols and the optimal therapy remains unclear, CHOP and CHOEP protocols represent the best choice according to experts ,34. HoweWe do not have reliable prognostic tools for this type of lymphoma, and the disease stage and International Prognostic Index (IPI) are not useful in predicting survival. Recently a new validated prognostic model, EATL prognostic index (EPI), was proposed to predict survival outcome in EATL and to select patients for new therapeutic strategies . This neIt seems reasonable that only the combination of clinicopathologic variables with molecular and genetic parameters can permit proper stratification of ITCL patients, favoring a more personalized therapeutic approach, keeping in mind that these conditions remain very aggressive with poor median OS (12 months).MEITL was the second-most common diagnosis in our cohort. Despite the clinical presentation overlap with EATL, histopathological analysis revealed some peculiarities. In fact, we found a positive correlation between the diagnosis of MEITL, the presence of angiotropism, and the expression of CD56. Angiotropism was previously described as a frequent feature in EATL, while we observed it in only 20% of our EATL cases compared to 80% of MEITL. On the contrary, CD56 expression in MEITL has been widely described, but it was never proved to be a specific marker of MEITL diagnosis.MYC gene) and recurrent mutations of STAT5b, JAK3, GNAI2, and SETD2. Intriguingly, the presence of (1) epitheliotropic pattern and angiotropism, (2) the frequent expression of CD8 and cytotoxic markers, (3) the evidence of recurrent mutation in JAK2 and STAT5b genes, (4) the involvement of epithelial interfaces, and (5) the very aggressive clinical behavior are common denominators between MEITL and aggressive epidermotropic cytotoxic T-cell lymphoma, a rare lymphoma involving the skin. Thus, it should be of interest to better understand the connections between these two rare lymphomas.MEITL seems to derive from “type B” intraepithelial effector memory T-cells, frequently expressing CD8α, together with CD3, CD7, CD56, and cytotoxicity markers. Moreover, MATK has been recently described as novel specific markers ,38. On aWe report how, in our case series, three out of five patients with MEITL had a diagnosis of CD. Even though both EATL and MEITL have a male predominance, two out of three of our MEITL patients with CD diagnosis were females. Clinically, they showed a clinical stage III in two cases and a clinical stage II in one, and they all died of disease. From a pathological point of view, all three of them showed a typical MEITL histology with the presence of a monomorphic infiltrate of CD3+, CD7+, CD56+, and CD5− cells with expression of cytotoxic molecules. Thus, despite the small number of cases, this finding seems to confirm our previous work showing that EATL and MEITL share some clinical and pathologic features and some chromosomal abnormalities that could justify, in the Caucasian population, the association of CD with both lymphoma subtypes . HoweverSTAT3-JAK2 gene fusion was described in CD4+ ITCLDGT [Our cases of ITCLDGT displayed many interesting features. Firstly, they all involved the stomach. Secondly, they also showed an association with some histopathological features, some of which have never previously been reported (the presence of many plasma cells within neoplastic infiltrate). It was also of great importance to notice that two out of three patients were initially diagnosed as EATL and then treated accordingly. This highlights that ITCLDGT diagnosis may be challenging, giving the higher frequency of aggressive ITCL and the absence of useful diagnostic markers. For this reason, considering the low number of our ITCLDGT patients, the significant features associated with this diagnosis in our study needs to be considered and validated in larger series. Recently, a specific  ITCLDGT ,41. We hDespite the longer survival described for this subtype of lymphoma, our three patients showed a median survival of 14 months, only slightly better than EATL. All three patients were diagnosed at an advanced stage and their death was associated with the course of the disease (not with complications or other causes).One patient with ITCLDGT had a diagnosis of CD, representing, to the best of our knowledge, the first described case of association. The heterogeneity of this entity could explain a possible association with CD, but further studies are needed to confirm this possibility.Similarly to ITCLDGT, ITCL-NOS is an exceedingly rare lymphoma of postulated peripheral T-cell origin (but possibly arising from innate T-resident lymphocytes). In our study, these lymphomas localized in the distal small bowel as well as in the large bowel, and behaved very aggressively, similarly to EATL or MEITL. Our ITCL-NOS cases did not display any specific clinical or histopathological features. This may be due to the fact that this is a basket category reflecting a still-unraveled biological heterogeneity.All in all, our study showed some limitations. First, the small number of cases, due to the rarity of the diseases, might have impaired the statistical analysis results. In particular, the aggressiveness of these lymphomas, resulting in high mortality, may have affected the survival analysis. Secondly, this retrospective study analyzed cases collected over a long time span, therefore we could not obtain complete data for all of our patients. Particularly, we could not biologically characterize peripheral lymphocytosis. Lastly, as previously reported, the association between CD and ITCL could have been underestimated, because the rapidly fatal course of these lymphomas may prevent, in some cases, achieving a complete work-up for CD diagnosis.Despite these limitations, our study is one of the largest ITCL case series reported in the current literature; thus, it may help to deepen our knowledge and to improve the management of these rare and only partially characterized lymphomas.In conclusion, primary ITCLs involving the small bowel are rare and frequently aggressive conditions, with many common clinical features but some different histopathological and molecular findings. Further studies on a larger number of patients are needed to better characterize these rare conditions, achieve better prognostic stratification, and improve the therapeutic approach.


Pharmacokinetics varies widely between children. Many factors play an important role in this variability, such as ontogeny, pharmacogenetics, gender, comorbidities, and drug-drug interactions. Significant work has already been done in adults to understand the impact of genetic polymorphisms on drug-metabolizing enzyme activity and drug response. Data remain poor in children due to ontogeny that impacts genotyping-phenotyping correlation and the difficulty enrolling children in prospective studies. Our study aimed to describe the use of cytochromes P450 (CYP) phenotyping and/or genotyping tests in children in a real-life setting and assess the correlation between the genotype and the phenotype. We reviewed the results of tests performed between January 2005 and December 2020. Fifty-two children were genotyped and/or phenotyped. Four patients were excluded from the present analysis as they only underwent ABCB1 genotyping, without CYP testing. Of the remainder, 18 underwent simultaneous CYP genotyping and phenotyping, while 17 underwent CYP genotyping only, and 13 underwent CYP phenotyping only. In all cases, investigations were performed after the following situations: insufficient clinical response to treatment, low plasma concentrations, and adverse drug reactions (ADR). The vast majority of cases were related to immunosuppressive or antipsychotic therapy. Genotyping and/or phenotyping explained or contributed to the aforementioned clinical events in 56% of cases. The correlation between the genotype and the phenotype showed variability depending on the assessed cytochrome. In several cases, the phenotype did not correspond to the genotype because of comedications. In conclusion, there is clearly value in guiding drug based on CYP activity in children. Children differ from adults not only in their growth in height and weight, but also in the rapid physiological, maturative, and developmental changes known as ontogeny. This results in a very heterogeneous population with wide variability in drug response .Physiological developmental changes occurring in children affects all pharmacokinetic processes, from absorption and distribution to metabolism and excretion, as well as the pharmacodynamic response . The impin vivo. The Geneva cocktail has been successfully used for years to measure the patients’ phenotype in our institution. This phenotyping cocktail is composed of seven low-dose specific probes for six different CYP and for P-glycoprotein (P-gp) (Cytochromes P450 (CYP) enzymes play a major role in drug metabolism and are among the most extensively studied DME in both adults and peadiatric populations. Drug-drug interactions involving CYP enzymes have received considerable attention for years . The mecn (P-gp) .In children, defining CYP activity and its impact on drug response is challenging. When considering existing approaches to determine DME activity, genotyping is limited due developmental regulation of gene expression, and phenotyping is made difficult by the necessity to administer a non-toxic exogenous probe for this population and the need to develop very sensitive analytical methods due to the small dose that can be administered . Our stuThis study is a paediatric subpart of three previously published studies that included children and adults . The stuIn this study, we evaluated in- and out-paediatric patients, aged 0–17 years, whose CYP genotyping or phenotyping tests were performed between January 2005 and December 2020 as part of their routine care. In Switzerland, genetic analyses fall under the Federal Act on Human Genetic Testing and as such may be performed only after having obtained written informed consent from parents/legal guardians  FOPH, 2. We reviGenotyping was performed by Geneva University Hospitals’ laboratory of molecular oncology and pharmacogenomics as described previously . GenotypPrediction of the phenotype based on the identified alleles was performed as described in our previous article  by usingPhenotyping was performed using exogenous oral enzyme-specific probes; namely, subtherapeutic doses of caffeine, bupropion, flurbiprofen, omeprazole, dextromethorphan, midazolam, and fexofenadine for CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, and P-glycoprotein activity assessment, respectively. The probes were administered orally on an empty stomach, either in the form of the Geneva cocktail (phenotyping cocktail approach) as described elsewhere  or by adconcordance when the measured phenotype was equal to the predicted phenotype. We concluded to non-concordance when the measured and predicted phenotypes were not equivalent. In these cases, we assessed the role of comedication and eventually concluded to drug-induced phenoconversion.Based on the identified alleles on genotyping, the patients were attributed to a predicted phenotype category. Based on the measured metabolic ratio on phenotyping, the patients were attributed to a measured phenotype. We concluded to We collected the main reason for genotyping/phenotyping, demographic data, and concomitant treatments. The reason for genotyping/phenotyping was one of the following: ADR/high drug levels, inefficacy/low drug levels, DDI, International Normalized Ratio (INR) variation, prescription (preemptive testing), and others. Based on the clinical pharmacology and toxicology consultation, two clinical pharmacologists concluded whether or not the results of the genotypic/phenotypic investigation explained the clinical situation.® software package, version 25  to perform the analyses. We concluded that genotype and phenotype were concordant when the measured phenotype corresponded to the predicted phenotype based on the alleles present. The cause of the non-concordance, including the presence of DDI, was investigated.We used descriptive statistics to report our data. We described categorical variables with frequencies, and continuous variables with means (± standard deviation). We used the SPSSA total of 52 children underwent genotype or phenotype testing during the study period. Since our study focused on genotype-phenotype concordance, four patients were excluded from this analysis as they were only tested for ABCB1 due to an inability to assess concordance with phenotype for this gene. The mean age of the remaining 48 patients was 9.7 (± 5.4) years (range: One month to 17 years). Of the 48 patients, 17 (35%) underwent genotyping only, 13 (23%) underwent phenotyping only, and 18 (42%) underwent simultaneous CYP genotyping and phenotyping.The mean age of the 17 children who were only genotyped was 8.3 ± 6.0 years (range: 0–16). Six of them were four years old or younger at the time of the investigation. We were unable to identify the reasons why phenotyping was not performed.The mean age of the 13 children who were only phenotyped was 11.8 ± 4.1 years. Except for one child aged 1 year, all were 9 years or older. We were unable to identify the reasons why only phenotyping was performed.A total of 18 children underwent simultaneous CYP genotyping and phenotyping. Seventeen had the same CYP isoenzyme simultaneously genotyped and phenotyped, while one patient had CYP2D6 genotyped but CYP2C9 phenotyped. The distribution of the predicted phenotype based on the genotype is presented in n = 17 + 18 = 35), the most frequently investigated enzyme was CYP2D6 (n = 21), followed by CYP2C19 (n = 14) and CYP3A5 (n = 11).Of all patients genotyped (n = 13 + 18 = 31), most received targeted phenotyping (n = 19) i.e., focusing on one, two, or eventually three CYP enzymes. Twelve patients received the full Geneva cocktail. The most frequently investigated enzyme was CYP3A4/5 (n = 27) followed by CYP2D6 (n = 23), particularly in the case of targeted phenotyping .Of all the patients who underwent phenotyping  on immunosuppressive therapy were mainly treated with tacrolimus (9/13) and were aged between 1 and 15 years. Eleven investigations were related to an antipsychotic treatment (risperidone or quetiapine). With the exception of one child aged 8 years, all others were adolescents aged 13 years or older.n = 27). In more than half of these cases (n = 15), the occurrence of ADR or high drug levels were the reasons for performing the tests. The involved drugs were mainly immunosuppressants followed by opioids and anticonvulsants. In the remaining 12 cases, insufficient therapeutic response or low drugs concentrations were the reasons. The involved drugs were mainly antipsychotics followed by immunosuppressants.Interestingly, genotyping or phenotyping results explained or contributed to the clinical event in 56% of cases  (https://www.knmp.nl/)  or to guide future treatment decisions (pre-emptive testing) . Organizgx.org/) , the Dutnmp.nl/) , the Phanmp.nl/) , and Ubinmp.nl/)  have relEvidence-based pharmacogenomic testing in children is less robust  and stilApart from being invasive, genotyping is easily performed in children of all ages. Genotyping results are immutable and independent of age. However, it does not consider the effect of gene ontogeny. The effect of a genotype variant depends on the expression of the gene. For this reason, in young children, depending on the developmental profile of the DME, the effect of the genotype may not be apparent . AnotherPhenotyping combines the effects of genetic, environmental, and developmental factors on CYP activity, and it therefore makes it possible to consider phenoconversion. It allows better prediction of the CYP activity at a given time point. However, it requires the administration of specific and non-toxic probes to children, followed by analysis of parent drugs and metabolites in biofluids. Validated MR interpretations are needed, in particular in children. The acceptability of oral probes in young children can be challenging . Thus, aOur study showed a highly variable concordance between genotype and phenotype in children. The lack of concordance occurred regardless of the age of the children and was, in half of the cases, for CYP2C19 and CYP3A5, explained by co-medication. For CYP2D6, the low sensitivity of genotyping tests to detect UM may have contributed to the non-concordant cases , as wellNo investigations were done preemptively before the initiation of treatment. They were all carried out to understand unexpected responses to a drug, its ineffectiveness or toxicity. Our study showed that the results of metabolic investigations could contribute to the clinical event in up to 60% of clinical situations.In conclusion, there is clearly value in a guided drug dosing based on CYP activity in children. However genetically based dosing algorithms used in adults cannot simply be extrapolated to young children, without considering the impact of ontogeny. Data describing the genotype-phenotype interaction in children are still scarce, particularly in sick and young children. Our study shows that genotyping and phenotyping are two complementary methods that can be used in children to determine CYP activity. The choice to perform genotyping, phenotyping or both should be considered on a case-by-case basis, taking into account their respective limitations, the clinical question and the patient. When used appropriately, both methods are helpful to understand interpatient variability in drug exposure and response, but probably also for guiding future treatments (pre-emptive testing).


Extraskeletal myxoid chondrosarcoma (EMC) is a rare malignant tumor described in the head and neck region, especially in the gingival. We present one case arising in the gingival of right mandible, and briefly reviewed the related literature.A 24-year-old male patient with a lesion of 3.5*2.0 cm in buccal gingival of right posterior mandible for 2 months. The tumor was composed of cartilaginous structures and myxoid matrix. Immunohistochemical(IHC) showed that the tumor cells to be positive for vimentin, focally positive for S-100, negative for calponin, SMA, SOX10. The Ki-67 labelling index was 80%. Fluorescent in situ Hybridization (FISH) was positive for NR4A3 rearrangement.Due to its unusual site and low incidence in the oral region, a combination of histological findings, immunohistochemistry, and molecular pathology as well as differential diagnosis with other diseases should be taken into consideration in the process of clinical diagnosis and treatment. Extraskeletal myxoid chondrosarcoma(EMC) is a rare malignant tumor accounting for less than 3% of all soft-tissue sarcomas , and maiA 24-year-old male patient with a 2-month history of a mass in buccal gingival of posterior mandible. The mass was about the size of a soybean and extended to the lingual side of the mandible, tough and hard in texture, with no significant clinical complaints, such as bleeding or numbness. After the biopsy, the tumor continued to enlarge rapidly and was accompanied with numbness and tenderness. The pathological results of the biopsy were low grade chondrosarcoma of osteogenic origin.Enhanced spiral Computed Tomography(CT) combined with Cone Beam Computed Tomography (CBCT) confirmed that the soft tissues of the labial buccal and lingual side of the right mandible were irregularly thickened, spanning the midline and reaching as far as the labial side of the right mandibular cuspid Fig. A and B. The patient underwent extensive resection of the sarcoma of the right mandible and segmental resection of the right mandible. Four months after surgery, recurrence occurred.The haematoxylin and eosin revealed that tumors cellswere round or slightly elongated of uniform shape and size with avariable amounts of mucoid matrix in a multinodular arrangement, and the tumor lesion presented a multinodular and lobular pattern with fibrous septa Fig. A, The ceThe immunohistochemical markers showed positive staining for vimentin, focally positive for P63, KRT14, S-100, Ki-67(80%) and showed negative staining for KRT5/6, KRT7, GFAP, cal-ponin, SMA, KRT-PAN, SOX10, mammaglobin  gene break two-color probe was used for FISH detection, and in this case FISH analysis showed rearrangement of NR4A3 , while females make up 37.5%(n = 18), and 2.1%(n = 1 case) was unavailable, the male-to-female ratio of about 1.5:1 . CMF is a benign bone tumor originating from cartilage tissue, which is more commonly seen in the metaphysis of long bones. CMF mainly affects the second and third decade of young adults . Around Odontogenic myxomas(OM). OM are rare benign tumors of mesenchymal origin. It most frequently occurs in the second to fifth decade of life and the average age of occurrence ranges from 23 to 30 years. Women are more commonly affected than men with a ratio of 1.5:1 , 20. TheMyxoid Liposarcoma(MLPS). Out of all liposarcomas, MLPSs occur in adolescents and young adults. It shows predilection for thigh . ChickenMyoepithelial carcinoma(MEC). MEC usually occur in young to middle-aged adults in the extremities and limb girdles, it tends to be identified more in the females. It is more frequently reported in major salivary glands, especially the parotid, it may also occur in the small salivary glands of the nasal cavity and palate. Architecturally, tumor cells may be arranged in solid, trabecular, cribriform, thin cords, small clusters, and tubular formations, showing a multinodular, lobulated, or sheet-like appearance  Fig. 9AA9A. HistOsteosarcoma(OST). OST mainly affects the metaphyseal growth plates in the long bones. OST of the jaw(OSJ) is rare, comprising of only 6% to 7% of all OST and 1% of all head and neck malignant neoplasms . OST oftChondroblastoma. Chondroblastoma is a benign, cartilage producing neoplasm. It most commonly affects the epiphyses of long bones. Craniofacial bones especially the temporal bones, are its favored site of occurrence, with the incidence ranging from 1%-7% of all chondroblastoma. It mostly affects patients in their first 2 decades of life . There iSynovial sarcoma(OST). Synovial sarcoma (SS) is a soft tissue malignant tumor. It primarily affects people in their thirties and most frequently occurs in the extremities (70%), followed by the trunk (15%), and least common in the head and neck region (5%–7%), the most common site of HNSS is the hypopharynx . It primImmunohistochemistry is an important aid in the diagnosis of this tumor. Neoplastic myoepithelial cells might show a variable staining pattern. Therefore, different myoepithelial markers should be analyzed, in order to confirm the origin when considering this diagnosis. Myoepithelial carcinoma usually stains positive for high molecular weight cytokeratins  and myoepithelial markers, such as smooth muscle actin (SMA), p63, S100, GFAP, and calponin. Most tumors are negative for CEA, KRT7, and EMA. FISH and/or gene rearrangement studies offer additional useful information in rendering an accurate diagnosis, the identification of a EWSR1 gene rearrangement or EWSR1 gene fusion may assist in the diagnosis of MEC .EMC is a rare entity which take place in the head and neck region, as for the intral-oral area such as the gingival present here, is extremely infrequent. Due to its scarcity of the intraoral area and the morphology mimicking of other mesenchymal origined neoplasms, the correct diagnosis of EMC is a great challenge for pathologists. Traditional single microscopic histology is considered to be the gold standard for the diagnosis of tumors. However, in this case, by a combination of histological findings, immunohistochemistry, and molecular pathology, a definitive diagnosis was made as EMC. After all, IHC and FISH have necessity to be taken more consideration into the diagnosis of tumors as long as the conditions acquired to gain more precision.


Limited investigation has been done on diet quality trajectories over adulthood. The main study objectives were to determine the diet quality group trajectories (GTs) over time and to detect changes in a socio-economically and racially diverse middle-aged cohort. Data from three waves of the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) study were used to determine diet quality with group-based trajectory modeling (GBTM). Three quality indices—the Healthy Eating Index (HEI), the Dietary Inflammatory Index (DII), and the Mean Adequacy Ratio (MAR)—were explored. The rate of change in quality over time was determined by mixed-effects regression analysis. Three diet quality GTs, low, middle, and high quality, were identified for each index and confirmed with spaghetti plots. Within each GT, only small changes in diet quality scores were observed, with improvements for the HEI and DII indices and a slight decline in MAR scores. Weighted kappa values revealed that the DII had better agreement with the HEI-2010 and MAR indices compared with the agreement between the HEI-2010 and MAR. Bayesian estimates revealed that the annualized rate of change in diet quality per person across the GTs was similar. There was minimal change in diet quality over time, regardless of the diet quality index used. Diet is a modifiable risk factor for several chronic conditions ,2,3,4. TThe group-based trajectory modeling (GBTM) method has been used to explore dietary pattern trajectories since 2014 ,14,18,20Dietary quality can be measured by different assessment tools. Although diet quality indices vary in scoring, all provide an overall picture of how a dietary pattern aligns with recommended food and/or nutrient intake guidance . These iWhen exploring the associations of diet with disease, changes solely in dietary behaviors can fail to detect relationships or attenuations of observed effects . AlthougThe HANDLS study design has been described in detail elsewhere ,33. Briev) 1, Wave 3 as v 2, and Wave 4 as v 3. Each participant provided written informed consent and was compensated monetarily. The study was conducted according to the guidelines of the Declaration of Helsinki, and the study protocol was approved by Human Institutional Review Board at the National Institutes of Health. The individuals in this study represent adults interviewed and examined in Waves 1, 3, and 4 of the HANDLS study (n = 2919) . Wave 1 Race was self-reported as African American or White, and sex at birth was coded as male or female. Participants were categorized as above or below poverty status defined by 125% of the 2004 U.S. Health and Human Services Poverty Guidelines at baseline enrollment . Educativ 1 of the HANDLS study, foods and beverages were coded using FNDDS 3.0 (2005–2006), for v 2, FNDDS 5.0 (2009–2010), and for v 3, FNDDS 2013–2014 [v 1 were collected in person. For v 2 and v 3, the first recall was obtained in person and the second by phone. Only those participants who completed two 24 hr dietary recalls were included in this study.This study implemented the same dietary assessment method at each visit. Dietary data in the HANDLS study were collected by trained interviewers using the USDA Automated Multiple-Pass Method (AMPM) for the 24 h recall . All foo013–2014 . Both reDietary Guidelines for Americans [The HEI-2010 is an index that measures compliance with the mericans . A detaimericans . The Natmericans . For eacThe inflammatory potential of the diet was calculated using 35 parameters. The parameters included energy, alcohol, protein, carbohydrate, dietary fiber, total fat, saturated fat, monounsaturated fat, polyunsaturated fat, omega 3 fatty acids, omega 6 fatty acids, cholesterol, 11 vitamins, 4 minerals, 6 flavonoid classes, caffeine, and tea. The original calculation by Shivappa et al. also included the following 10 parameters: trans fatty acids, garlic, ginger, onion, pepper, rosemary, saffron, thyme/oregano, turmeric, and eugenol . These wNutrient-based diet quality was assessed using the MAR, which is calculated from Nutrient Adequacy Ratios . Nutrientraj and trajplot Stata plugins for estimating GBTM were used to create the diet quality trajectories [Multiple imputations  were conducted using chained equations for the non-exposure and non-outcome variables with missing data. Using data from all 3 visits, the ectories ,46. The ectories , which iTIME) with two-way interaction terms between sociodemographic covariates and TIME. Additional models assessing stability included diet quality trajectories among covariates, which also interacted with TIME. A reduced model with only linear TIME as the predictor for each diet quality index was used in order to obtain an empirical Bayes estimator for annualized rate of change per individual for each diet quality index. Square and cubic terms were included to allow the comparison of BIC using a similar criterion as for GBTM. Models were run for the overall sample, by sex, and by race. Spaghetti plots were presented using a 10% simple random sample of the participants in the final analytic sample (See The mixed-effects regression models (mixed command in Stata) were run using the diet trajectory groups, adjusting for age (centered at visit 1), sex, race, and poverty status. All models incorporated number of years elapsed between visits , 53.0 ± 0.2 y at v 2 (n = 2377), and 56.6 ± 0.2 y at v 3 (n = 2156). Over half the sample were women, African American adults, and had completed high school or more education. Approximately 40% of the overall sample was below the poverty line. The percentage was higher for women compared with men and for African Americans compared with White adults  scores of the HEI diet quality index at visits 1, 2, and 3 were 42.6 ± 0.3, 46.3 ± 0.3, and 48.7 ± 0.3, respectively. The mean HEI-2010 scores ranged from 42–49 out of a maximum of 100 at each visit, indicating only generally poor adherence to the The GBTM analyses revealed three trajectory groups for each of the diet quality indices explored . These tThe mean (±SE) diet quality scores by trajectory for each visit are provided in As shown in The findings for the DII revealed that approximately one-third (32.3%) of the HANDLS sample was defined by the pro-inflammatory diet depicted by the red trajectory. The direction of the DII scores is the reverse of the HEI and MAR, with high scores indicating a poor-quality diet. In comparison, an estimated 10.1% of the sample consumed a diet with low-inflammatory potential , as depicted by the green color in −9 for group 1, 3.8 × 10−9 for group 2, and 4.2 × 10−9 for group 3, which suggested the slopes do not change and SDs are extremely small and can be considered 0.The trajectory for low diet quality assessed by MAR scores was comprised of approximately 29.9% of the sample depicted in Scatterplot matrices were generated to display how each of the diet quality indices at each visit were correlated with each other and with the probability of belonging to the most unhealthy diet quality group  See . Overallp = 0.007), indicating that there were significant differences in the rate of diet quality change between this group trajectory and the low diet quality trajectory. For the DII index, a different interaction, time with high diet quality, was found significant . Significant interactions were found for both the middle and high diet quality groups with time for the MAR index. The β (±SE) coefficient for the middle quality interaction with time was −0.390 (0.090) (p < 0.001), and for the high quality it was −0.583 (0.099) (p < 0.001). Compared with the low diet quality group, the rates of decline varied and could be described as unstable. The full models were adjusted for age at v 1, race, sex, and poverty status. The results of the mixed-effects regression analyses provide an assessment of the stability of the diet quality trajectories over time, defined as the number of years between visits . For eacWith respect to the DII and MAR indices, the odds of belonging to either the middle or high diet quality group trajectory versus the low diet quality group were greater for men compared with women, lower among African American adults compared with White adults, and lower among individuals living below poverty compared with those living above poverty . This study is unique with respect to the diet quality indices chosen to be examined. Each index provided a picture of a different aspect of the quality of the dietary patterns associated with a sample that is underrepresented in the nutrition literature. Yet GBTM yielded three dietary pattern groups for each index, revealing low, medium, and high dietary quality. Based on these trajectories, changes in dietary quality over time were successfully evaluated.Within each group’s trajectory, there appear to be only small changes in diet quality scores over the past 13 years. The annualized rate of change in diet quality per person was similar given the 95% CI for the Bayesian estimates of the means across the group trajectories within each diet quality index. The observed changes were consistent with the findings of other researchers, despite differences in dietary collection methods. Mertens et al. reported positive 1.83 and 2.81 HEI-2010 scores, based on 3-day records, over 10 years in a Flemish sample of men and women, 18–75 years, respectively . The dieThe mixed-model regression results of this study revealed changes in diet quality over time for all indices. No consistent trend was observed across indices. Even though this change was statistically significant, the actual point value change in scores was small and may not be of practical clinical significance. These small but inconsistent changes are likely associated with volatility in the prices and availability of foods, especially because participants were not systematically retested at the same time of year, making it impossible to adjust for seasonal variations.The Dietary Patterns Method Project provided researchers with evidence of consistent classifications of adults between pairs of diet quality indices such as the HEI-2010 and Dietary Approach to Stop Hypertension (DASH) . In thisEven though the HEI and DII scores showed improvement over time, it is evident that participants in the HANDLS study could further improve the quality of their diets by making different food and beverage choices. The groups at higher risk for lower diet quality were those below poverty status, African American adults, and women. Similar to our findings, others reported that non-Hispanic Blacks had lower diet quality (HEI-2015) than non-Hispanic White adults, but they found that women had significantly higher HEI scores than men . These rDietary Guidelines for Americans is associated with a lower risk of total mortality from cardiovascular disease, cancer, and respiratory diseases in different racial and ethnic groups [Dietary Guidelines for Americans, was launched. Yet, between 2017 and 2020, only 25.3% of the participants in the National Health and Nutrition Examination Survey reported they were aware of the existence of MyPlate, and fewer (8.3%) used MyPlate to follow dietary recommendations [There is evidence that greater adherence to the c groups . In 2011ndations . If morendations . For heaThis study has strengths and limitations. First, we utilized longitudinal data over a 10- to 12-year span from a biracial sample underrepresented in the literature to determine the diet quality trajectories. At each visit, 24 h recalls were collected on separate days, resulting in the representation of weekdays and weekend days in the dataset. The AMPM, a validated recall method that reduces measurement error in dietary data collection , was useIn conclusion, three diet quality trajectories, specifically low, middle, and higher quality, were identified for each quality index explored. Mixed-effects regression analyses provided evidence of a significant but minimal change in diet quality over time, regardless of the diet quality index used. These consistencies in the results suggest that a single assessment may be sufficient to characterize typical patterns.


Altered Immunoglobulin G (IgG) N-glycosylation is associated with aging, inflammation, and diseases status, while its effect on esophageal squamous cell carcinoma (ESCC) remains unknown. As far as we know, this is the first study to explore and validate the association of IgG N-glycosylation and the carcinogenesis progression of ESCC, providing innovative biomarkers for the predictive identification and targeted prevention of ESCC.In total, 496 individuals of ESCC (n=114), precancerosis (n=187) and controls (n=195) from the discovery population (n=348) and validation population (n=148) were recruited in the study. IgG N-glycosylation profile was analyzed and an ESCC-related glycan score was composed by a stepwise ordinal logistic model in the discovery population. The receiver operating characteristic (ROC) curve with the bootstrapping procedure was used to assess the performance of the glycan score.In the discovery population, the adjusted OR of GP20 , IGP33 , IGP44 , IGP58 , IGP75 , and the glycan score are 4.03 , 0.69 , 0.56 , 0.52 , 7.17 , and 2.86 , respectively. Individuals in the highest tertile of the glycan score own an increased risk (OR: 11.41), compared with those in the lowest. The average multi-class AUC are 0.822 (95% CI: 0.786-0.849). Findings are verified in the validation population, with an average AUC of 0.807 (95% CI: 0.758-0.864).Our study demonstrated that IgG N-glycans and the proposed glycan score appear to be promising predictive markers for ESCC, contributing to the early prevention of esophageal cancer. From the perspective of biological mechanism, IgG fucosylation and mannosylation might involve in the carcinogenesis progression of ESCC, and provide potential therapeutic targets for personalized interventions of cancer progression. Esophageal cancer (EC) is the seventh most common cancer type worldwide and ranks sixth in the cause of cancer-related death . In ChinMost patients of ESCC lack obvious symptoms at the early stage and progress insidiously to a relatively advanced stage when detected . TherefoThe glycomics analysis is a promising ‘omics’ technology , providiOur previous study found that the IgG N-glycosylation profiles were independently associated with the esophageal precancerosis for squamous cell carcinoma beyond inflammation . HoweverIn total, 516 subjects voluntarily participated in this study and 496 individuals were finally recruited in the analysis according to the inclusion and exclusion criteria as shown in The following were the inclusion criteria: (1) providing informed consent prior to enrollment; (2) initial confirmed diagnosis of precancerosis or ESCC, or neither; (3) the required information and data of IgG glycosylation profile eligible. The exclusion criteria were as follows: (1) diagnosis of other gastrointestinal cancer  before or at the screening; (2) history of mental illness, infectious disease, autoimmune diseases or and other malignant cancers; (3) women in pregnancy or lactation; (4) post-operation or post-radiochemotherapy.The study was approved by the independent ethics committee of National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (grant number: 17–124/1380) and ethics committee of Capital Medical University (grant number: Z2019SY012). All participants provided their written informed consents before taking part in this study.The diagnosis of precancerous esophageal lesions and early ESCC was according to the endoscopic screening and biopsy examination, while the judgment of the controls was only based on the endoscopic diagnosis. In a previous article we described the procedures of routine endoscopy examination . The con2 (in meters squared) and the participants were grouped into <24 kg/m2 and ≥24 kg/m2. Systolic blood pressure (SBP) and diastolic blood pressure (DBP) were measured twice on the right arm using a standard mercury sphygmomanometer in a sitting position after the subjects had rested at least 10 minutes, and the mean value was used for the present analysis. Hypertension was defined as a self-reported history of hypertension, a mean SBP ≥140 mmHg or DBP ≥90 mmHg or taking antihypertensive medications. Education level was classified into illiteracy, primary school, middle or high school, bachelor degree or above. Marriage status was defined as married status or others. Family income was divided into less than and more than 50,000 yuan per capita per year. Smoke was defined as at least one cigarette per day in the past year, while drink was defined as at least 100 ml consumption of alcohol (content ≥50%) per day in the past year. Dietary frequency of pickled food, fried food, hot food and mildew food were grouped into never, seldom and often. History of gastrointestinal disease involved gastroenteritis and peptic ulcer. Family history of gastrointestinal cancer included esophageal cancer, gastric cancer and intestinal cancer.The body mass index (BMI) was defined as weight (in kilograms)/heightThe glycosylation experiment and analysis involved four key processes: IgG isolation and purification from plasma, glycans enzyme digestion and release, fluorescence labeling and quantitative detection, as described previously , 33. In N-acetylglucosamine (GlcNAc), core fucosylation and mannose. The amounts of GP and IGP were normalized followed by log transformation and batch-effect was considered and corrected. The detailed structural and biological information of each GP and IGP was shown in Finally, 24 direct glycan peaks (GPs) were quantitatively expressed with the percentage of the total integrated peak area, as presented in Continuous variables adhering to the normal distribution were represented as mean and standard deviation (SD), and the differences between groups were tested by the independent ANOVA tests; otherwise, the median and interquartile range  were used, and the differences were explored by Kruskal-Wallis H tests. Categorical variables were presented as n (%), and the differences were tested by the chi-square tests. The box plots were used to show the differences of IgG GPs and IGPs among the controls, precancerosis and early ESCC.The false discovery rate (FDR) correction was used to primarily identify the substantially increased or decreased IgG glycans and traits associated with ESCC. Then, the candidate glycans and traits selected above were finally confirmed using the stepwise ordinal logistics regression according to Akaike information criterion (AIC), which composed of an ESCC-related glycan score by the regression coefficients. The glycan score and its components were tested both in the discovery and validation population after the confounding covariates adjusted in three models: model 1 was unadjusted; model 2 was adjusted for age and sex; model 3 was further adjusted for BMI, hypertension, smoke, drink, education, income, marriage status and dietary habits. Formula of the ESCC-related glycan score was listed below:n × amounts of each IgG GP and IGP n), where β is the ordinal logistics coefficient.Score = ∑(βThe discriminative capacity of the proposed ESCC-related glycan score was illustrated using multi-class receiver operating characteristic (ROC) curve, and the average area under-the curve (AUC) value was provided. Significant differences in the proposed ESCC-related glycan score between different groups in the discovery and validation populations were subsequently assessed using DeLong’s test. The robustness of the ESCC-related glycan score was assessed using a bootstrap procedure (k=100). The bootstrap method was used to resample distinct data sets 100 times from the original data set, and the number of subjects in each resampled data set was set to be the same number as the sample size of the original data set. SNPs associated with the proposed ESCC-related glycan score were found out by Meta-analysis of the IgG N-glycosylation GWAS and were annotated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis were carried as well as protein–protein interaction (PPI) network analysis to find potential hub genes. Finally, we validated the potential hub genes on The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) based on RNA sequence data. Detailed statistical methods are provided in the Supplementary material online. All statistical tests were two-sided at a significant level of 0.05, and the Benjamini-Hochberg method was applied to control the FDR for multiple hypothesis tests . All theIn the discovery population, the median  age was 58.50 , and 163 (46.84%) were males. In the validation population, the median  age was 60.00 , and 65 (43.92%) were males. The characteristics were similar between the discovery and validation populations, except age as shown in The detailed distribution of IgG glycans and traits among the controls, precancerous and early ESCC groups were shown in We screened ESCC-related N-glycan alterations based on ordinal logistic regression analysis. Regression coefficients were used to estimate odds ratios for each of the independent variables. The mathematic formula named ESCC-related glycan score was constructed to differentiate ESCC from esophageal precancerosis and controls (ESCC-related glycan score = 0.612×GP20 - 0.357×IGP33 - 0.623×IGP44 - 0.439×IGP58 + 1.333×IGP75). The distinct distribution of the ESCC-related glycan score was shown in After linkage disequilibrium, we found 27 SNPs were associated with the proposed ESCC-related glycan score and 15 of them could be annotated to functional genes  and the derived traits  were primarily selected and validated to be associated with different stages of ESCC. Specific IgG N-glycosylation pattern participates in the carcinogenesis progression of ESCC, and the proposed ESCC-related glycan score could be a novel indicator. Variation in the fucosylated glycans and the suppressed mannose level, reflected by the altered glycans and traits, could be potential intervention target for ESCC. In addition, an ESCC-related glycan score was composed in this study, which achieved a high AUC value to discriminate different stages of ESCC. Besides, SMARCB1, IKZF1, RUNX1, TAB1, RUNX3, B4GALT1 were considered as potential hub genes of the proposed ESCC-related glycan score.In our study, we found that GP20 and IGP75 was positively associated with ESCC progression, while IGP33, IGP44 and IGP58 was negatively associated . These results above revealed a glycosylation pattern of increased digalactosylated biantennary glycan, the incidence of bisecting GlcNAc in all fucosylated digalactosylated glycans, and decreased high mannose glycan, fucosylated glycan, the ratio of all fucosylated monosyalilated and disialylated glycan among ESCC.These finding were largely in consistent with previous studies. Liu et al. reported a significantly decreased of mannose glycan in patients with colorectal cancer  and we fin vitro that knockdown of IKZF1 decreases the expression of fucosyltransferase FUT8, resulting in increased levels of fucosylated glycans, and suggest that RUNX1 and RUNX3, together with SMARCB1, regulate expression of glycosyltransferase MGAT3 (Our study found SMARCB1, IKZF1, RUNX1, TAB1, RUNX3 and B4GALT1 as potential hub genes for the proposed ESCC-related glycan score, which were in agreement with previous studies. B4GALT1, IKZF1, TAB1 and SMARCB1 are reported to associate with IgG N-glycosylation show pleiotropy with autoimmune diseases and haematological cancers , while Sse MGAT3 .in vivo or in vitro will be conducted to confirm the association of IgG N-glycans biomarkers with the carcinogenesis progression of ESCC. Third, our study was based on two Chinese populations, more collaborations are needed to validate the generalizability of the observed results for other ethnic groups. Fourth, the identification and quantification of glycans were by HPLC in our study, although glycan standards were used, additional cross validation with other techniques, e.g. mass spectrometry, lectin array will be performed in our further research.In this study we explored the significant differences in IgG N-glycosylation profile among early ESCC, esophageal precancerosis, and the controls. To our knowledge, this is the first attempt aiming at the association of IgG N-glycans biomarkers with the carcinogenesis progression of ESCC. The identified glycans and proposed glycan score were validated in another population. However, the limitations should be addressed. First, the sample size was relatively small causing an inadequate statistical power. Second, this was a population-based cross-sectional study, hence, no causal relationships or pathophysiological inferences were available, basic experiments In summary, we have performed the first analysis so far to identify the association of IgG N-glycans biomarkers with the carcinogenesis progression of ESCC. In this study, GP20, IGP33, IGP44, IGP58, IGP75 are significantly associated with the carcinogenesis progression of ESCC, and the proposed glycan score is a novel indicator for different progressive stages. In addition, the variation of fucosylation level and the suppressed mannose level could provide potential therapeutic intervention targets. These findings support the potential utility of glycomics in the ESCC related personalized therapy. The mechanism studies about the biological or pathological function of the fucosylated protein and mannosed protein in the carcinogenesis of ESCC and other cancers are of paramount importance. The experiment on mice after knocking out the corresponding genes of glycosyltransferase and glycosylhydrolase regulating the fucosylation and mannose levels are the next step for our study to validate the effect of IgG N-glycan patterns in the carcinogenesis of ESCC. Future studies on larger cohorts from diverse populations are expected for the validation of these observed associations.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.The studies involving human participants were reviewed and approved by the Independent Ethics Committee of National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College and the Ethics Committees of Capital Medical University. The patients/participants provided their written informed consent to participate in this study.XG and GW contributed to conception and design of the study. DZ, ZYZ, YQL, ZZ, ZW, JZ, YuL, YoL, and HZ collected the data. HP, ZL, WF, XTL, and YXL performed the statistical analysis. HP and ZW wrote the first draft of the manuscript. LT, XW, XY, and FZ wrote sections of the manuscript. All authors contributed to the article and approved the submitted version.


Breast cancer is the most common cancer and the most common cause of cancer death in women. Although survival rates have improved, unmet psychosocial needs remain challenging because the quality of life (QoL) and QoL-related factors change over time. In addition, traditional statistical models have limitations in identifying factors associated with QoL over time, particularly concerning the physical, psychological, economic, spiritual, and social dimensions.This study aimed to identify patient-centered factors associated with QoL among patients with breast cancer using a machine learning (ML) algorithm to analyze data collected along different survivorship trajectories.The study used 2 data sets. The first data set was the cross-sectional survey data from the Breast Cancer Information Grand Round for Survivorship (BIG-S) study, which recruited consecutive breast cancer survivors who visited the outpatient breast cancer clinic at the Samsung Medical Center in Seoul, Korea, between 2018 and 2019. The second data set was the longitudinal cohort data from the Beauty Education for Distressed Breast Cancer (BEST) cohort study, which was conducted at 2 university-based cancer hospitals in Seoul, Korea, between 2011 and 2016. QoL was measured using European Organization for Research and Treatment of Cancer QoL Questionnaire Core 30 questionnaire. Feature importance was interpreted using Shapley Additive Explanations (SHAP). The final model was selected based on the highest mean area under the receiver operating characteristic curve (AUC). The analyses were performed using the Python 3.7 programming environment (Python Software Foundation).The study included 6265 breast cancer survivors in the training data set and 432 patients in the validation set. The mean age was 50.6 (SD 8.66) years and 46.8% (n=2004) had stage 1 cancer. In the training data set, 48.3% (n=3026) of survivors had poor QoL. The study developed ML models for QoL prediction based on 6 algorithms. Performance was good for all survival trajectories: overall (AUC 0.823), baseline (AUC 0.835), within 1 year (AUC 0.860), between 2 and 3 years (AUC 0.808), between 3 and 4 years (AUC 0.820), and between 4 and 5 years (AUC 0.826). Emotional and physical functions were the most important features before surgery and within 1 year after surgery, respectively. Fatigue was the most important feature between 1 and 4 years. Despite the survival period, hopefulness was the most influential feature on QoL. External validation of the models showed good performance with AUCs between 0.770 and 0.862.The study identified important factors associated with QoL among breast cancer survivors across different survival trajectories. Understanding the changing trends of these factors could help to intervene more precisely and timely, and potentially prevent or alleviate QoL-related issues for patients. The good performance of our ML models in both training and external validation sets suggests the potential use of this approach in identifying patient-centered factors and improving survivorship care. Breast cancer is the most common cancer and the most common cause of cancer death in women worldwide . In the To develop tailored interventions and to provide appropriate survivorship care, it is necessary to find predictors for QoL during different phases of survivorship ,5. AlthoTo overcome the limitation of traditional models, a few machine learning (ML) models have been proposed in the literature that predict the QoL of breast cancer survivors. However, there were only a few ML models for QoL prediction with limitations ,8-12. FiTo produce a robust tool to identify factors associated with QoL during different survival phases, 2 different data sets were used. These included (1) the cross-sectional survey data from the Breast Cancer Information Grand Round for Survivorship (BIG-S) study to develop a model and (2) the longitudinal cohort data from the Beauty Education for Distressed Breast Cancer (BEST) cohort study to validate the model.The BIG-S study recruited consecutive breast cancer survivors (BCS) who visited the outpatient breast cancer clinic at the Samsung Medical Center in Seoul, Republic of Korea, between November 2018 and April 2019. The BIG-S study included survivors aged over 20 years and who did not have secondary cancer, metastasis, or recurrence. A total of 6265 survivors agreed to participate in the BIG-S study: before surgery (n=1980) and 1 year (n=653), 2 years (n=1265), 3 years (n=921), 4 years (n=682), and 5 years (n=764) after surgery.The BEST study (n=432) was conducted at 2 university-based cancer hospitals in Seoul, Republic of Korea, to evaluate the effect of cancer treatment-induced altered body image and QoL. Subjects were eligible to participate if they were between 18 and 65 years of age, had a diagnosis of breast cancer , had no sign of metastasis, were expected to have breast cancer surgery, and did not receive preoperative chemotherapy or radiation therapy . There wIn this study, the target variable was poor QoL, which was measured using a 7-point Likert scale with the European Organization for Research and Treatment of Cancer (EORTC) QoL Questionnaire Core 30 questionnaire. The single item has been validated to measure overall QoL .To determine the factors associated with QoL, information about sociodemographics; diagnosis and treatment; and physical, psychological, social, and spiritual well-being was included based on a literature review  data preprocessing, (2) training ML models, (3) model evaluation and selection, (4) model interpretation, and (5) external validation . The tarTo train the ML models, the feature selection method and the recursive feature elimination method based on the Shapley Additive Explanation (SHAP) method were used to reduce the model complexity and to remove unnecessary features that generate noise in the prediction model. The SHAP method is one of the explainable artificial intelligence methods . ThroughTo validate and evaluate the model, 10-fold stratified cross-validation was used. The entire training data set was divided into 10-fold equal size subsamples by stratifying for the outcome variables. A single subsample was retained as the validation data for testing the model, and the remaining 9 subsamples were used as training data and the process was repeated 10 times. Using the 10 cross-validation results, the area under the receiver operating characteristic curve (AUC) scores were averaged for each model, and the final model with the highest mean AUC was selected. In this study, we also used SHAP values to interpret feature contributions and assess the clinical significance of predictive models. According to a previous study, the SHAP value is the measurement of the marginal contribution of each feature in different combinations. The SHAP value of a feature can be interpreted as the difference between the model’s predicted value when that feature is included versus when it is excluded, taking into account all possible combinations of other features. The base value, on the other hand, is the average predicted value of the model for all samples. When the SHAP value of a feature is positive, it means that including that feature has a positive effect on the predicted value, while a negative SHAP value indicates a negative effect. Overall, SHAP values help to explain how each feature contributes to the model’s predictions, providing insight into the model’s decision-making process ,22.Finally, external validation was confirmed using the BEST cohort data set, which was a completely different data set from that used for model training. The poor QoL group was predicted by inputting the external validation data set into the final model that trained the entire training data set using the ML algorithm selected by the survival period. It is notable that between the 3- and 4-year models, there was no validation data set because there was no participant follow-up within the BEST cohort for these time periods. The validation performances were also evaluated using AUC, accuracy, F1 score, sensitivity, and specificity, and were also compared with training performance.All analyses were performed in the Python 3.7 programming environment (Python Software Foundation) and used the scikit-learn package and TensorFlow Keras framework.The study was approved by the institutional review board of the Samsung Medical Center, Seoul, Republic of Korea, in the development set (SMC-2018-08-070) and external validation set (SMC-2011-07-019). Informed consent was obtained from all study participants.All 6265 participants were included in the full analysis data set. The mean age of the study participants was 50.6 (SD 8.66) years and 46.8% (n=2004) of participants were stage 1. In the training data set, 48.3% (n=3026) of the participants were classified into the poor QoL group . The proIn the validation set, the mean age was 46.5 (SD 7.87) years, and 47.1% (n=428) of the participants were stage 1  was the most important feature, and fatigue, side effects, physical function, emotional function, and role function were also important features. By the survival period, menopause symptoms  and emotional function  were the most important features prior to breast cancer surgery (Table S6 in All 5 model evaluation metric averages calculated in the external validation set were higher than 0.7 .For external validation, the receiver operating characteristic curves for each survival period were used to calculate the AUC. When the final trained models for each survival period were externally validated using the BEST data set, the validation AUC was between 0.770 and 0.862, and the differences from the results of the 10-fold stratified cross-validation for training were from 0.009 to 0.056 .In this study, we developed and validated factors associated with QoL including physical, psychological, economic, spiritual, and social dimensions by survivorship trajectory using an ML algorithm. The developed model and external validation model performance were good for all survival trajectories. Before surgery, menopause symptoms and emotional function were important features. Within 1 year after the surgery period, physical function was the most important feature. Between 1 and 4 years, fatigue was the most important feature. Regardless of the survival period, hopefulness was the most influential feature of spiritual well-being.In this study, the AUC for evaluating model performances surpassed 0.8 for all survival periods, and the results of external validation using data collected in other studies were also greater than 0.77. This performance is much better than that of previous studies that predicted QoL using ML modeling, which reported values ranging from 0.476 to 0.793 . These MPrior to breast cancer surgery, menopause symptoms and emotional function were selected as important features that affect QoL in BCS. Among menopause symptoms, the most important factor was in the psychological domain, which included depressive mood, irritability, and anxiety. According to a previous study, depression and anxiety are the 2 most common psychiatric comorbidities encountered in patients with breast cancer ,7. PatieIn this study, physical function was the most important feature that affected QoL in the group that was within 1 year after breast cancer surgery. This result was consistent with previous reports that BCS are susceptible to physical functioning–related problems and often experience treatment-related declines in their physical functioning capabilities within the 1-year period following their cancer diagnosis . TreatmeBetween 1 and 4 years after breast cancer surgery, fatigue is the most important feature that affects QoL in BCS. Cancer-related fatigue is one of the most distressing and common posttreatment sequelae among survivors of early-stage breast cancer . More thHopefulness was the most important feature in all survival period models, especially, between 4 and 5 years. Spiritual well-being was a predictor of improved QoL and is one of the important outcomes to measure in BCS . PreviouIn this study, we performed an external validation to test the generalizability of our models, which is a strength compared to the previous study that did not perform external validation ,9-12. ThThis study has several limitations. First, it is a cross-sectional study, and the directions of the associations between QoL; symptoms; and physical, psychosocial, and spiritual functions could be interchangeable. In fact, patients who had a poor QoL might report poorer function status. Second, QoL was measured using a single item from the EORTC-C30, and this might not be a reliable method to measure an individual’s QoL. However, this single question has been validated to measure a person’s overall QoL, and it has been widely used in different cultures and countries, including Korea. Lastly, the results of our study might not be generalizable to other cancer survivors in other settings. Further studies with various types of cancer survivors are necessary to confirm the study findings and its generalizability.Despite these limitations, this study had several strengths. First, we included physical, psychological, economic, spiritual, and social dimensions and clinical factors. Second, we developed a prediction model to predict QoL from pretreatment to 5 years after surgery. Third, we developed different ML-based QoL surveillance models across survivorship. Fourth, we used SHAP methods, which allow for the interpretation of the model by the reader. Fifth, we performed external validation and the models showed good performance.The results of this study may provide valuable information on developing a patient-centered survival care plan. Understanding the changing trends of influencing factors associated with QoL during different survival trajectories could help health care professionals intervene timely and appropriately in order to prevent or alleviate factors more precisely.


Introduction: Mitochondrial DNA depletion syndrome type 3 is an emerging disorder linked to variants in the deoxyguanosine kinase gene, which encodes for mitochondrial maintenance. This autosomal recessive disorder is frequent in the Middle East and North Africa. Diagnosis is often delayed due to the non-specificity of clinical presentation with cerebro-hepatic deterioration. The only therapeutic option is liver transplantation, although the value of this remains debatable.Methods: We describe the clinical, biochemical, and molecular profiles of Lebanese patients with this rare disorder. We also present a review of all cases from the Middle East and North Africa.Results: All Lebanese patients share a unique mutation, unreported in other populations. Almost half of patients worldwide originate from the Middle East and North Africa, with cases reported from only 7 of the 21 countries in this region. Clinical presentation is heterogeneous, with early-onset neurological and hepatic signs. Liver failure and lactic acidosis are constants. Several variants can be identified in each population; a unique c.235C>T p. (Gln79*) pathogenic variant is found in Lebanese patients. Outcome is poor, with death before 1 year of age.Conclusion: The pathogenic nonsense variant c.235C>T p. (Gln79*) in the deoxyguanosine kinase gene may be considered a founder mutation in Lebanon. Further genotypic delineation of this devastating disorder in populations with high consanguinity rates is needed. DGUOK) gene is a nuclear gene, mapped to chromosome 2p13  maintenance defects are emerging genetic disorders encompassing multiple mtDNA deletion and mtDNA depletion syndromes (MTDSs) resulting from qualitative and quantitative defects in mtDNA synthesis, respectively. Depending on the underlying enzymes involved, mtDNA maintenance defects are categorized into several types of disorder: mtDNA synthesis, mitochondrial nucleotide salvage pathway, cytosolic nucleotide metabolism, mitochondrial nucleotide import, and mitochondrial fusion disorders. These rare disorders are caused by pathogenic variants in one of the 20 nuclear genes encoding proteins implicated in mtDNA maintenance . They arome 2p13 , encodinactivity  and syntactivity  of the r pathway .Most MTDS type 3 patients show multisystem involvement, with a variable combination of digestive and neurologic manifestations associated with impaired growth . AntenatDGUOK gene mutations; however, whole-exome sequencing is more frequently used by physicians to reach the diagnosis in view of the non-specificity of the presenting clinical symptoms. To date, per the Human Gene Mutation Database, 57 disease-causing variants in the DGUOK gene are known, with most being missense and nonsense mutations. Outcome is usually poor, with death occurring before 4 years of age , have previously been reported [by More than 100 patients with MTDS type 3 have been reported so far . Cases forted by .DGUOK variant, which remains unreported in other populations.We describe the clinical, biochemical, and molecular profiles of three other Lebanese patients with this unique A retrospective review of the charts of patients diagnosed with MTDS type 3 at the American University of Beirut Medical Center (AUBMC) was conducted. The collected data included initial clinical manifestations; biochemical, radiological, and genetic investigations; and outcome. For genetic testing, samples were sent to Centogene laboratory, Germany, for next-generation sequencing. The generated library was sequenced, at this reference laboratory, on an Illumina platform to obtain at least 20× coverage depth for >98% of the targeted bases. At Centogene, variants with low quality and/or unclear zygosity are confirmed by orthogonal methods. Consequently, specificity of >99.9% for all reported variants is achieved.An analysis of clinical, biochemical, and molecular data for all MTDS type 3 patients from the MENA region, including the Lebanese patients, is also presented.Written informed consent was obtained from the legal guardians/parents of the patients for participation in this study and for the publication of any potentially identifiable data included in this article, in accordance with our institutional requirements and the Declaration of Helsinki.Patient 1 was a female infant born at term, the product of 39 weeks of gestation, to a primigravida 29-year-old mother, with a birth weight of 1855 g, length 44 cm, and head circumference 31 cm; all parameters were below 1% No perinatal complications were noted. Parents were consanguineous, with positive family history of death in early infancy of two male cousins with undiagnosed liver disease , consistent with the genetic diagnosis of autosomal recessive MTDS type 3. Both parents were heterozygous carriers of this mutation. Sanger sequencing was not performed by Centogene, since the identified variant was of good quality. The patient passed away 1 month later, in septic shock and with severe lactic acidosis.atient 1 , was a 2atient 1 . Whole-ePatient 3, maternal niece of patient 1 and cousin of patient 2 , whereas nystagmus was a less constant finding (79%). The majority were diagnosed before 6 months of age and died before 1 year of age. All five reported Lebanese patients exhibited early-onset hepatic and neurological symptoms, before 2 months of age. Intrauterine growth retardation, low birth weight, and subsequent failure to thrive were present in all three patients. Outcomes were poor and death occurred within 5 months of age, with the exception of one patient who died at 11 months of age.The biochemical hallmark was lactic acidosis associated with hepatic cytolysis, hypoglycemia, and cholestasis in all patients. Serum alpha-fetoprotein levels were elevated, in parallel to hypertyrosinemia, in all patients in the Israeli Druze cohort, two Saudi patients , and the three Lebanese patients reported in this study.Genetic profiling of MTDS type 3 patients reported in the MENA region revealed a total of seven variants, mostly nonsense mutations (89%) . The mosThe exact incidence or prevalence of MTDP type 3 in different populations is not yet known; however, this disorder seems to be more prevalent in the MENA region, and specifically in countries with high rates of consanguineous marriage, as in Lebanon .DGUOK deficiency, with rapid hepatic and neurological deterioration, as reported in other patients carrying null mutations  in the DGUOK gene variant, unique to Lebanese patients and as yet unreported in any other population, may be considered a founder mutation in Lebanon. Further delineation of genotypic variants in populations with high consanguinity rates, as in the MENA region, is important for genetic counseling and pre-implantation diagnosis.This