Multimodal Early Birth Weight Prediction Using Multiple Kernel Learning.

In this work, a novel multimodal learning approach for early prediction of birth weight is presented. Fetal weight is one of the most relevant indicators in the assessment of fetal health status. The aim is to predict early birth weight using multimodal maternal-fetal variables from the first trimester of gestation (Anthropometric data, as well as metrics obtained from Fetal Biometry, Doppler and Maternal Ultrasound). The proposed methodology starts with the optimal selection of a subset of multimodal features using an ensemble-based approach of feature selectors. Subsequently, the selected variables feed the nonparametric Multiple Kernel Learning regression algorithm. At this stage, a set of kernels is selected and weighted to maximize performance in birth weight prediction. The proposed methodology is validated and compared with other computational learning algorithms reported in the state of the art. The obtained results (absolute error of 234 g) suggest that the proposed methodology can be useful as a tool for the early evaluation and monitoring of fetal health status through indicators such as birth weight.

Placental Microarray Profiling Reveals Common mRNA and lncRNA Expression Patterns in Preeclampsia and Intrauterine Growth Restriction.

Preeclampsia (PE) and Intrauterine Growth Restriction (IUGR) are major contributors to perinatal morbidity and mortality. These pregnancy disorders are associated with placental dysfunction and share similar pathophysiological features. The aim of this study was to compare the placental gene expression profiles including mRNA and lncRNAs from pregnant women from four study groups: PE, IUGR, PE-IUGR, and normal pregnancy (NP). Gene expression microarray analysis was performed on placental tissue obtained at delivery and results were validated using RTq-PCR. Differential gene expression analysis revealed that the largest transcript variation was observed in the IUGR samples compared to NP (n = 461; 314 mRNAs: 252 up-regulated and 62 down-regulated; 133 lncRNAs: 36 up-regulated and 98 down-regulated). We also detected a group of differentially expressed transcripts shared between the PE and IUGR samples compared to NP (n = 39), including 9 lncRNAs with a high correlation degree (p < 0.05). Functional enrichment of these shared transcripts showed that cytokine signaling pathways, protein modification, and regulation of JAK-STAT cascade are over-represented in both placental ischemic diseases. These findings contribute to the molecular characterization of placental ischemia showing common epigenetic regulation implicated in the pathophysiology of PE and IUGR.

Key Clinical Factors Predicting Adipokine and Oxidative Stress Marker Concentrations among Normal, Overweight and Obese Pregnant Women Using Artificial Neural Networks.

Maternal obesity has been related to adverse neonatal outcomes and fetal programming. Oxidative stress and adipokines are potential biomarkers in such pregnancies; thus, the measurement of these molecules has been considered critical. Therefore, we developed artificial neural network (ANN) models based on maternal weight status and clinical data to predict reliable maternal blood concentrations of these biomarkers at the end of pregnancy. Adipokines (adiponectin, leptin, and resistin), and DNA, lipid and protein oxidative markers (8-oxo-2'-deoxyguanosine, malondialdehyde and carbonylated proteins, respectively) were assessed in blood of normal weight, overweight and obese women in the third trimester of pregnancy. A Back-propagation algorithm was used to train ANN models with four input variables (age, pre-gestational body mass index (p-BMI), weight status and gestational age). ANN models were able to accurately predict all biomarkers with regression coefficients greater than R² = 0.945. P-BMI was the most significant variable for estimating adiponectin and carbonylated proteins concentrations (37%), while gestational age was the most relevant variable to predict resistin and malondialdehyde (34%). Age, gestational age and p-BMI had the same significance for leptin values. Finally, for 8-oxo-2'-deoxyguanosine prediction, the most significant variable was age (37%). These models become relevant to improve clinical and nutrition interventions in prenatal care.

MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes.

SUMMARY: The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories. AVAILABILITY: Marker-gene database tool: http://ibb.uab.es/mgdb

Effect of late-onset fetal growth restriction on organization of behavioral state in infants.

BACKGROUND: The aim of this study was to analyze whether late-onset fetal growth restriction (FGR) alters regulatory capability in infants, and whether this can be detected using both the neonatal behavior assessment scale (NBAS) and brainstem auditory-evoked potentials (BAEP). METHODS: The diagnosis of FGR was made on Doppler examination in the third trimester of pregnancy. NBAS and BAEP measurement were performed at 1 month of corrected postnatal age. RESULTS: The group with late-onset FGR was integrated with 17 infants and the control group consisted of 14 subjects. The NBAS range of state score, which reflects organization of behavioral state, was low in infants with late-onset FGR. No differences were found in BAEP between groups. No association between NBAS and BAEP was detected. CONCLUSION: Late-onset FGR has a deleterious effect on NBAS range of state, but possibly does not alter BAEP response. It is proposed that regulatory capabilities in the neonatal period play a primary role in subtle cognitive difficulties in infants with late-onset FGR in the long term.

Behavioural fever is a synergic signal amplifying the innate immune response.

Behavioural fever, defined as an acute change in thermal preference driven by pathogen recognition, has been reported in a variety of invertebrates and ectothermic vertebrates. It has been suggested, but so far not confirmed, that such changes in thermal regime favour the immune response and thus promote survival. Here, we show that zebrafish display behavioural fever that acts to promote extensive and highly specific temperature-dependent changes in the brain transcriptome. The observed coupling of the immune response to fever acts at the gene-environment level to promote a robust, highly specific time-dependent anti-viral response that, under viral infection, increases survival. Fish that are not offered a choice of temperatures and that therefore cannot express behavioural fever show decreased survival under viral challenge. This phenomenon provides an underlying explanation for the varied functional responses observed during systemic fever. Given the effects of behavioural fever on survival and the fact that it exists across considerable phylogenetic space, such immunity-environment interactions are likely to be under strong positive selection.

Association between selected structural defects and chromosomal abnormalities.

OBJECTIVE: To determine the association between some major structural abnormalities detected prenatally by ultrasound and chromosomal abnormalities. MATERIAL AND METHODS: The present study was a retrolective, transversal study. We analyzed case records of patients during the fetal follow-up at the Department of Maternal Fetal Medicine from January 1994 to May 2010 to identify fetal patients with a diagnosis of holoprosencephaly, diaphragmatic hernia, omphalocele, cystic hygroma, hydrops and cardiac defects. We analyzed patients who had a prenatal invasive diagnosis procedure to obtain the odds ratio (OR) for some major isolated anomalies and their different combinations with respect to chromosomal abnormalities. RESULTS: We examined 280 patients with ultrasonographic markers for chromosomal alteration, 197 met inclusion criteria, from which 88 had chromosomal abnormalities. The most frequent diagnosis was trisomy 18 (31.8%), which was followed by trisomy 21 (21.6%), trisomy 13 (21.6%), Turner syndrome (monosomy X) (14.8%) and other chromosomal abnormalities (10.2%). Among the fetuses with nonisolated holoprosencephaly, we obtained an OR of 4.9 95% CI (0.99-24.2) for aneuploidy. Associated omphalocele had an OR of 7.63 95% CI (2.07-46.75), p < 0.01. Interestingly, 62% of aneuploidy cases had associated cardiac defects [OR = 7.7 95% CI (1.4-41.7)]. In addition, associated cystic hygroma had an OR of 2.5 95% CI (0.59-10.91). Heart defects were the most common defects in fetuses with trisomy 18 (57.1%), when they were associated with facial cleft, we had an OR of 11.08 95% CI (2.99-41.11), p < 0.0001. Statistical potency was calculated for each analyzed defect and it was over 80% for all of them but diaphragmatic hernia. CONCLUSIONS: The association of 2 or more structural defects increased the probability of a fetus to be a carrier of a chromosomal disorder; however this was not statistically significative except for associated omphalocele. Heart defects showed the greatest association with all chromosomal abnormalities. The most important association was among heart defect, facial cleft and trisomy 13.

Amniotic band sequence: prenatal diagnosis, phenotype descriptions, and a proposal of a new classification based on morphologic findings.

OBJECTIVE: The aim of this study is to describe the phenotype of fetuses affected by amniotic band sequence (ABS) that were diagnosed at the Instituto Nacional de Perinatología Isidro Espinosa de los Reyes and to propose a new classification based on morphologic findings. MATERIAL AND METHODS: Cases with a final diagnosis of amniotic band sequence, diagnosed between January 1993 and July 2010 in the Department of Maternal Fetal Medicine, were reviewed. Demographic, clinical, and periconceptional data were collected, and the defects were described and classified. The association frequencies of the defects were also determined. RESULTS: We included 50 cases with prenatal diagnosis of amniotic band sequence. The mean maternal age was 25.7 ± 6.9 years. Of these patients, 54% (27/50) were primiparous compared to 22% (11/50) who had three or more previous pregnancies. Craniofacial defects were seen in 78% (39/50) of the cases, followed by defects of the extremities 70% (35/50), abdominal wall, spine, and/or thorax 52% (26/50). The most frequent defects were the following: a) Encephalocele and facial clefts in the craniofacial group. b) Shortening at any level in the limb defects group, and c) Alterations of the spinal column curvature in the group of "other" defects. CONCLUSIONS: The amniotic band sequence shows a tendency to affect women who are in their earlier years of reproduction. We observed an inverse relationship between the number of pregnancies and the frequency of presentation of this pathology. The majority of affected fetuses showed a phenotype that fit into one of many groups. Therefore, we propose classifying the amniotic band sequence phenotypes into the following groups: I. Craniofacial defect + limb defect. II. Craniofacial defect + limb defect + abdominal wall, spinal column, and/or thoracic defects. III. Limb defect + abdominal wall, spinal column, and/or thoracic defects; and IV. Isolated defect (craniofacial, limb, or thoraco-abdominal wall). This classification system will be helpful in diagnosing amniotic band sequence. Based on future research studies, we hope that we can use this classification system as a prognosis fetal factor to establish a more accurate fetal prognosis and recurrence probability. Finally, we created a flowchart describing all of the steps that were followed by our Department from the moment an amniotic band was found by ultrasound until the definitive diagnosis was made and the follow up according to the fetal findings.

Role of Moonlighting Proteins in Disease: Analyzing the Contribution of Canonical and Moonlighting Functions in Disease Progression.

The term moonlighting proteins refers to those proteins that present alternative functions performed by a single polypeptide chain acquired throughout evolution (called canonical and moonlighting, respectively). Over 78% of moonlighting proteins are involved in human diseases, 48% are targeted by current drugs, and over 25% of them are involved in the virulence of pathogenic microorganisms. These facts encouraged us to study the link between the functions of moonlighting proteins and disease. We found a large number of moonlighting functions activated by pathological conditions that are highly involved in disease development and progression. The factors that activate some moonlighting functions take place only in pathological conditions, such as specific cellular translocations or changes in protein structure. Some moonlighting functions are involved in disease promotion while others are involved in curbing it. The disease-impairing moonlighting functions attempt to restore the homeostasis, or to reduce the damage linked to the imbalance caused by the disease. The disease-promoting moonlighting functions primarily involve the immune system, mesenchyme cross-talk, or excessive tissue proliferation. We often find moonlighting functions linked to the canonical function in a pathological context. Moonlighting functions are especially coordinated in inflammation and cancer. Wound healing and epithelial to mesenchymal transition are very representative. They involve multiple moonlighting proteins with a different role in each phase of the process, contributing to the current-phase phenotype or promoting a phase switch, mitigating the damage or intensifying the remodeling. All of this implies a new level of complexity in the study of pathology genesis, progression, and treatment. The specific protein function involved in a patient's progress or that is affected by a drug must be elucidated for the correct treatment of diseases.

AI-Enhanced Analysis Reveals Impact of Maternal Diabetes on Subcutaneous Fat Mass in Fetuses without Growth Alterations.

Pregnant women with diabetes often present impaired fetal growth, which is less common if maternal diabetes is well-controlled. However, developing strategies to estimate fetal body composition beyond fetal growth that could better predict metabolic complications later in life is essential. This study aimed to evaluate subcutaneous fat tissue (femur and humerus) in fetuses with normal growth among pregnant women with well-controlled diabetes using a reproducible 3D-ultrasound tool and offline TUI (Tomographic Ultrasound Imaging) analysis. Additionally, three artificial intelligence classifier models were trained and validated to assess the clinical utility of the fetal subcutaneous fat measurement. A significantly larger subcutaneous fat area was found in three-femur and two-humerus selected segments of fetuses from women with diabetes compared to the healthy pregnant control group. The full classifier model that includes subcutaneous fat measure, gestational age, fetal weight, fetal abdominal circumference, maternal body mass index, and fetal weight percentile as variables, showed the best performance, with a detection rate of 70%, considering a false positive rate of 10%, and a positive predictive value of 82%. These findings provide valuable insights into the impact of maternal diabetes on fetal subcutaneous fat tissue as a variable independent of fetal growth.

Prenatal prevalence of skeletal dysplasias and a proposal ultrasonographic diagnosis approach.

OBJECTIVE: To determine the prevalence of fetal bone dysplasias diagnosed at the Department of Maternal Fetal Medicine (UNIMEF) of the Instituto Nacional de Perinatologia (INPer); and to describe the most frequent skeletal dysplasias and to propose a diagnostic flow chart. MATERIALS AND METHODS: This is a case series study including skeletal dysplasias cases from January 1995 until December 2009 at the UNIMEF Statistical analysis was performed using SPSS 12 statistical software. RESULTS: A total of 81,892 births were registered at the institution during the study period. The prevalence of bone dysplasia was 8.1 per 10,000 births. We used a diagnostic flow chart that was developed at our institution to diagnose skeletal dysplasias. Micromelia (n = 40, 59.7%) and both rhizomelia and mesomelia (n = 17, 25.3%) were highly prevalent. We found other structural anomalies in 40 cases (61.1%), which were associated with different skeletal dysplasias; these other anomalies were mainly congenital heart diseases (12 cases) with a predominance of ventricular septal defects. There was polyhydramnios in 43.2% of cases. The mean of the gestational age at diagnosis was 24.5 weeks (SD 5.66). The karyotype was obtained in 11.9% (8/67) of cases. A total of 7 stillbirths and 11 neonatal deaths were registered, of which only 10 cases received a necropsy. Births occurred in the third trimester for 88% of cases, of which 85% were born via Cesarean section, whereas in the second trimester, the vaginal approach was chosen in 100% of cases. CONCLUSIONS: The prenatal diagnosis of bone dysplasias is challenging due to the late development of the diagnostic features. Nevertheless, using ultrasonography in a systematic approach, in conjunction with a multidisciplinary approach, is a key factor in the diagnosis of this disease during the fetal period.

Major craniofacial defects: case series and prenatal diagnosis at the Instituto Nacional de Perinatología, Mexico.

OBJECTIVE: To describe the prenatal diagnosis, characteristics, development, perinatal outcome, and final diagnosis of pregnancies complicated by fetuses with major craniofacial defects, at the Instituto Nacional de Perinatologia, México, 1997-2008. MATERIAL AND METHODS: A retrospective, descriptive study from January of 1997 to January 2008, analyzed 152 pregnancies complicated by fetuses with major craniofacial defects, diagnosed at the Department of Fetal Medicine of the National Institute of Perinatology. Data were obtained from patients clinical records. RESULTS: . The mean age was 28 +/- 8 years, with the largest number of cases between 20 and 24. The mean gestational age at diagnosis was 27.5 +/- 6.4 gestational weeks. The average termination of pregnancy was at 35 +/- 5 gestational weeks. In 43.4% of cases there were no major structural defects associated with the facial defect. The most commonly associated structural alterations were cerebral, cardiac, and limb abnormalities. Karyotyping was performed in only 57 cases, and was abnormal in 25. CONCLUSIONS: Structural ultrasound should be performed on all pregnant women between weeks 18 and 24 for detection of major craniofacial defects. Where defects are found, a thorough review of other structures should be carried out to determine whether the defects are syndromic. A systematic and multidisciplinary approach is essential to providing the best care and appropriate advice to parents.

Inflammatory-Metal Profile as a Hallmark for COVID-19 Severity During Pregnancy.

Pregnancy makes women more susceptible to infectious agents; however, available data on the effect of SARS-CoV-2 on pregnant women are limited. To date, inflammatory responses and changes in serum metal concentration have been reported in COVID-19 patients, but few associations between metal ions and cytokines have been described. The aim of this study was to evaluate correlations between inflammatory markers and serum metal ions in third-trimester pregnant women with varying COVID-19 disease severity. Patients with severe symptoms had increased concentrations of serum magnesium, copper, and calcium ions and decreased concentrations of iron, zinc, and sodium ions. Potassium ions were unaffected. Pro-inflammatory cytokines IL-6, TNF-α, IL-8, IL-1α, anti-inflammatory cytokine IL-4, and the IP-10 chemokine were induced in the severe presentation of COVID-19 during pregnancy. Robust negative correlations between iron/magnesium and zinc/IL-6, and a positive correlation between copper/IP-10 were observed in pregnant women with the severe form of the disease. Thus, coordinated alterations of serum metal ions and inflammatory markers - suggestive of underlying pathophysiological interactions-occur during SARS-CoV-2 infection in pregnancy.

Accuracy of different equations for estimating fetal weight.

OBJECTIVE: To evaluate the accuracy of ten equations based on ultrasound parameters for estimating fetal weight (FW). STUDY DESIGN: A cross-sectional study was performed in 250 healthy women with normal singleton pregnancies between 34 and 41 weeks of gestation. FW estimations calculated according to ten different equations were compared against birth weight (BW) which was determined within 72 h after FW estimation. Estimated error rate, intraclass correlation coefficient, and agreement between BW and FW calculated by each formula were analyzed. RESULTS: Most of the formulas were inaccurate in predicting BW, only 2 formulas showed less than 10% of the measurements lying within the 10% of estimated error. Four formulas tended to overestimate, while six tended to underestimate FW. CONCLUSIONS: Appropriate equations for estimating FW in all populations should be developed. However, where there are no local growth curves, the accuracy of the available fetal growth equations should be tested.

[Laser ablation of the placental vascular anastomoses for the treatment of twin-to-twin transfusion syndrome]. / Fotocoagulación láser de las comunicaciones vasculares placentarias en el tratamiento del síndrome de transfusión feto-fetal.

AIM: To report the experience of the intrauterine treatment of monochorionic biamnotic (MC/BA) twin pregnancies complicated with twin-to-twin transfusion syndrome (TTTS) applying laser ablation of the placental vascular anastomoses (LAPVA). MATERIAL AND METHODS: During 18 months period 35 MC/BA twin pregnancies were treated. TTTS was diagnosed based on the discrepancies in amniotic fluid and bladder size between both twins. Severity of TTTS was classified according to the hemodynamic changes in both twins. LAPVA was performed between 16-26 weeks of gestation using a rigid straight fetoscope and a YAG (neodymium: yttrium aluminium garnet) laser equipment. Survival was considered when the neonate was home discharged. RESULTS: Overall survival was 62.8% (44/70 fetuses). In 77% of pregnancies (27/35) at least one twin survived, and in 48.5% (17/35) of cases both twins survived. Bleed was the most frequent complication (12/35; 34%). In 5 cases there was severe bleeding leading to late premature rupture of membranes and death of both twins. Median time stay in the neonatal intensive care unit was 20 days (range, 7-120). There were no signs of brain damage at the time of discharge. CONCLUSION: These results are similar to those already published. Bleeding was the most frequent complication, however as the experience improved it was less frequent. Overall success is highly associated with a good neonatal care support.

[Diffuse cavernous hemangioma of the uterus diagnosed during pregnancy. Case report]. / Hemangioma cavernoso difuso del utero diagnosticado durante el embarazo. Reporte de un caso.

We report the case of a pregnancy of 16 weeks with anemia and a presumptive diagnosis of partial mole. In secondary care this diagnosis was ruled out through ultrasonography and diffuse cysts were found in the myometrium. Spectral Doppler ultrasound showed no flow, but it could be observed with power angiography. Cesarean section was performed at 38 weeks and hysterectomy 24 hours after because of intra-abdominal hemorrhage. Power angiography, spectral Doppler and serum human chorionic gonadotropin are the most useful diagnostic tools in the differential diagnosis of diffuse cavernous hemangioma of the uterus. Postpartum hemorrhage is a likely complication.

Genotoxicity Associated with Residual Monomers in Restorative Dentistry: A Systematic Review.

PURPOSE: Incomplete polymerisation processes produce several leachable substances. The aim of this work was to review, through existing research and published literature, the genotoxic effect of residual monomers of polymers used in restorative dentistry. MATERIALS AND METHODS: The selection of published studies was performed on six databases from January 2000 to June 2020. The keywords used were: 'genotoxicity' or 'DNA damage' and 'dental resin' or 'methacrylates' or 'residual monomers'. The selection was carried out according to the parameters and guidelines of the Preferred Reporting Items for Systematic Review and Metanalyses (PRISMA) and was based on patient, intervention, comparison, and outcome (PICO). The inclusion criteria were: in vitro and in vivo studies published in English that evaluated genotoxicity for residual monomers leached from polymers related to restorative dentistry. Case reports and review articles were excluded. RESULTS: Twenty-seven studies met the eligibility criteria. Two categories were constructed based on the experimental design, in vivo and in vitro reports. For the in vitro research, two main methods of assessing DNA damage were reported in selected studies: micronucleus (MN) counting and alkaline comet assay. For in vivo reports, the main method for assessing genotoxic damage was MN counting. CONCLUSION: From the electronic search, structured data extraction, and analysis by different independent reviewers, results from the present systematic review allow us to conclude that DNA damage is induced by monomers/co-monomers (triethylene glycol dimethacrylate, bisphenol-A-glycidyl methacrylate, urethane dimethacrylate, and 2-hydroxyethyl methacrylate) that are used in restorative dentistry. This systematic review highlights the need for more research on the use of monomers/co-monomers to properly assess clinical biocompatibility.

Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer.

Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.

Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models.

BACKGROUND: The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Here we tested in vivo selection of anti-EGFR SR tumors in CRC patient-derived xenograft (PDX) models as a strategy for a molecular dissection of SR mechanisms. METHODS: We analyzed 21 KRAS, NRAS, BRAF, and PI3K wildtype CRC patient-derived xenograft (PDX) models for their anti-EGFR sensitivity. Furthermore, 31 anti-EGFR SR tumors were generated via chronic in vivo treatment with cetuximab. A multi-omics approach was employed to address molecular primary and secondary resistance mechanisms. Gene set enrichment analyses were used to uncover SR pathways. Targeted therapy of SR PDX models was applied to validate selected SR pathways. RESULTS: In vivo anti-EGFR SR could be established with high efficiency. Chronic anti-EGFR treatment of CRC PDX tumors induced parallel evolution of multiple resistant lesions with independent molecular SR mechanisms. Mutations in driver genes explained SR development in a subgroup of CRC PDX models, only. Transcriptional reprogramming inducing anti-EGFR SR was discovered as a common mechanism in CRC PDX models frequently leading to RAS signaling pathway activation. We identified cAMP and STAT3 signaling activation, as well as paracrine and autocrine signaling via growth factors as novel anti-EGFR secondary resistance mechanisms. Secondary resistant xenograft tumors could successfully be treated by addressing identified transcriptional changes by tailored targeted therapies. CONCLUSIONS: Our study demonstrates that SR PDX tumors provide a unique platform to study molecular SR mechanisms and allow testing of multiple treatments for efficient targeting of SR mechanisms, not possible in the patient. Importantly, it suggests that the development of anti-EGFR tolerant cells via transcriptional reprogramming as a cause of anti-EGFR SR in CRC is likely more prevalent than previously anticipated. It emphasizes the need for analyses of SR tumor tissues at a multi-omics level for a comprehensive molecular understanding of anti-EGFR SR in CRC.

Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer.

Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.