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73 citation(s) found for "Urrutia, Raúl".

A Novel De Novo STAG1 Variant at the RAD21 Binding Interface Is Associated With Hypoglycemia, Recurrent Fever, Immunodeficiency and Features of Classical Cohesinopathies
Hussain, Hafiz Muhammad Jafar , Zimmermann, Michael T. , Farris, Joseph , Panwar, Deepak , Thurman, Sarah , Muthusamy, Karthik , Wick, Myra , Klee, Eric W. , Zimmermann, Michael T , Safgren, Stephanie L , Farris, Joseph D , Panwar, Deepak , Thurman, Sarah Allen , Muthusamy, Karthik , Urrutia, Raul , Vairo, Filippo , Klee, Eric W , Safgren, Stephanie L. , Urrutia, Raúl , Vairo, Filippo Pinto e

Mayo Clinic

Clinical Genetics | September 9, 2026 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.1111/cge.70246 | PMID 42713681 Get It

ABSTRACT The cohesin complex, composed of SMC1, SMC3, RAD21, and STAG1/STAG2, is essential for chromosome cohesion, DNA repair, and transcriptional regulation. Pathogenic variants in cohesin components cause cohesinopathies. The classical characteristics of cohesinopathies include developmental delay (DD), intellectual disability (ID), feeding difficulties, hypotonia, short stature, hearing loss, and dysmorphic features. Here, we present a 5‐year‐old boy with classical cohesinopathy features, including DD/ID and feeding difficulties, along with non‐classical features such as hypoglycemia, recurrent fever, and immunodeficiency. Trio exome sequencing identified a novel de novo missense variant of uncertain significance (NM_005862.3:c.643G>A(p.Val215Ile)) in the STAG1 gene. The variant localizes to the RAD21 interaction interface, and molecular dynamics (MD) simulations revealed conformational changes comparable to other STAG1 variants reported as likely pathogenic in patients, supporting a deleterious effect which may disrupt the STAG1‐RAD21 interaction interface. This case expands the phenotypic and molecular spectrum of STAG1‐related cohesinopathy and advances our understanding of the disease mechanism.
Mutant KRAS Heterogeneity Shapes Nuclear Architecture During Pancreatic Cancer Initiation
Pollin, Gareth , Leverence, Elise, Assuncao, Thiago M. de , Iovanna, Juan, Hong, Johnny C. , Zimmermann, Michael T. , Urrutia, Raúl , Lomberk, Gwen , Mathison, Angela J , Zimmermann, Michael T , Urrutia, Raul , Lomberk, Gwen L , Mathison, Angela , Iovanna, Juan

Mayo Clinic

Epigenomes | March 10, 2026 | Volume: 10 | Issue: 1 | Pages: 19

10.3390/epigenomes10010019 | PMID 41892368 Get It

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) arises predominantly from activating KRAS mutations, yet individual genetic variants differ markedly in signaling output and clinical impact. G12D, the most prevalent variant, strongly drives oncogenic programs, whereas G12R signals less efficiently through the AKT and ERK pathways and is associated with longer patient survival than G12D-driven PDAC. Methods: To elucidate how these differences influence early cellular transformation, we expressed a panel of KRAS mutants in non-cancerous pancreatic ductal epithelial cells as a model of early PDAC initiation and profiled transcriptional and phospho-proteomic responses. We next examined whether epigenetic differences translate into mutation-specific changes in nuclear organization using quantitative imaging of G12D- and G12R-expressing nuclei at 24 and 48 h. Results: Each variant established a unique regulatory program enriched for chromatin remodelers, histone modifiers, and nuclear structural factors, indicating that variant-specific KRAS signaling rapidly develops divergent epigenetic states. Integrated transcriptomic and phospho-proteomic analyses identified G12D and G12R as the most divergent variants. G12D induced pronounced nuclear remodeling, including increased nuclear size, irregular morphology, and reorganization of the nucleolus and spliceosome, consistent with extensive chromatin and transcriptional reprogramming. In contrast, G12R elicited a weaker response, with minimal or delayed structural changes. Conclusions: Together, these findings demonstrate that KRAS mutational context in pancreatic ductal epithelial cells shapes early transcriptional reprogramming that actively remodels nuclear architecture and nuclear sub-compartments. This work establishes nuclear structural remodeling as a structural state of KRAS-driven epigenetic dysregulation during PDAC initiation.
Outcomes of patients (pts) with higher-risk myelodysplastic syndromes (HR-MDS) treated with hypomethylating agents (HMA) + venetoclax (VEN) – a large analysis from the international consortium for MDS (icMDS) validate database
Ali, Najla Al , Stein, Eytan M. , Brunner, Andrew M. , McMahon, Christine M. , Shallis, Rory M. , Hawkins, Hayley, Chandhok, Namrata S. , Logothetis, Constantine , Bidikian, Aram, Getz, Theodore, Harris, Amyah, Amaya, Maria , Ball, Somedeb , Grenet, Justin , Haferlach, Torsten , Maciejewski, Jaroslaw P. , Sallman, David A. , Al-Rabi, Kamal , Halahleh, Khalid , Pleyer, Lisa , Pappa, Vassiliki, Consagra, Angela , Al‐Kali, Aref , Stahl, Max, Bewersdorf, Jan Philipp , Kewan, Tariq Zuheir , Lanino, Luca , Wei, Wei , Dezern, Amy Elizabeth , Sekeres, Mikkael A. , Uy, Geoffrey L. , Urrutia, Samuel , Carraway, Hetty E. , Desai, Pinkal , Griffiths, Elizabeth A. , Zeidner, Joshua F. , Savona, Michael R. , Roboz, Gail J. , Rolles, Benjamin , Wang, Eunice S. , Xie, Zhuoer , Madanat, Yazan F. , Abaza, Yasmin , Campos, Jaclynn, Badar, Talha , Enjeti, Anoop Kumar , Hiwase, Devendra , Díez‐Campelo, María , Valcárcel, David , Haferlach, Claudia , Kotsianidis, Ιoannis , Pappa, Vasiliki , Santini, Valeria , Ogawa, Seishi , Nannya, Yasuhito , Stahl, Max, Porta, Matteo Giovanni Della , Komrokji, Rami S. , Zeidan, Amer M.

Mayo Clinic

Blood | December 4, 2025 | Volume: 146 | Issue: Supplement 1 | Pages: 606-606

10.1182/blood-2025-606 Get It

Abstract Introduction: HMA monotherapy (HMAm) continues to be the standard of care for HR-MDS. While the addition of VEN to azacitidine (AZA) improved overall survival (OS) and complete remission (CR) rates among older pts with acute myeloid leukemia (AML) over AZA monotherapy, the recently completed phase III VERONA trial of AZA+/-VEN in HR-MDS failed to show an OS benefit for AZA/VEN over AZA monotherapy. Using the icMDS VALIDATE database, we compared outcomes of pts with HR-MDS treated with HMA or HMA/VEN as frontline therapy. Methods: The icMDS VALIDATE database includes over 4000 adult MDS pts who received HMA-based therapy from 32 international centers in 9 countries. For this analysis, we included pts with HR-MDS defined by International Prognostic Scoring System [IPSS] ≥1.5 or IPSS-revised [IPSS-R] ≥4 (at diagnosis or HMA initiation) and treated with HMAm or HMA/VEN as frontline therapy for HR-MDS. We assessed responses based on IWG 2023 criteria (Zeidan A et al, Blood 2023). Composite complete remission (cCR) was defined as CR+CRbi+CRuni+CRh+CRequivalent. We calculated OS from time of HMA initiation to date of death from any cause. Pts lost to follow-up were censored at the date they were last known to be alive. We used Kaplan-Meier methods to calculate OS and compared OS between different groups using the log-rank test. We used Cox and logistic regression models to adjust for baseline prognostic variables as appropriate. The study was funded by an independent grant from Abbvie. Results: A total of 1907 pts met eligibility and were included (1552 AZA, 221 decitabine, 134 HMA+VEN). 479 pts subsequently underwent allogeneic stem cell transplant (allo-SCT; 430 after HMAm [32.6%]; 49 after HMA/VEN [37.1%]). Our cohort was enriched for pts with adverse disease characteristics including complex karyotype (33.6%) and TP53 mutations (28.7%). Compared to pts treated with HMA/VEN, pts treated with HMAm were more likely to be male (p=0.012), have lower baseline platelet counts (p=0.037), peripheral blood (PB) blasts (p=0.004), or bone marrow blasts (p<0.001), and were less likely to have very high risk IPSS-M (p<0.001), TP53 mutations (p<0.001), or complex karyotype (p=0.020). In unadjusted analyses, the rate of cCR was significantly lower in HMAm treated pts compared to HMA/VEN treated pts (27.7% vs. 48.8%, p<0.001). However, CR rate was not significantly different (11.7% vs. 17.1% for HMAm and HMA/VEN, respectively, p=0.22). After adjusting for age, sex, and IPSS-M, pts treated with HMA/VEN were more likely to achieve cCR compared to HMAm with an odds ratio (OR) of 2.49 (95% CI: 1.56-3.96, p<0.001). When separated by TP53 mutation status, the OR for cCR for HMA/VEN vs HMAm was 4.17 (95%CI: 2.14-8.31; p<0.001) and 1.27 (95%CI: 0.54-2.86; p=0.57) for TP53 wild-type and TP53-mutant pts, respectively. In unadjusted analyses, median OS was 17.4 months for HMAm and 19.6 months for HMA+VEN, and OS did not differ significantly by treatment type (p=0.33). For HMAm treated pts, the OS rates at year 1, 2, 3 were 0.65 (95%CI: 0.63-0.67), 0.38 (95%CI: 0.36-0.40), and 0.27 (95%CI: 0.25-0.29), respectively. For HMA/VEN treated pts, the OS rates at year 1, 2, 3 were 0.64 (95%CI: 0.56-0.73), 0.45 (95%CI: 0.36-0.56), and 0.37 (95%CI: 0.27-0.51), respectively. In a multivariate analysis adjusting for age, sex, PB blast, IPSS-M and allo-SCT as a time-varying covariate, treatment with HMA/VEN vs HMAm did not significantly influence OS (hazard ratio (HR) of OS for HMA/VEN vs HMAm: 0.89, 95%CI: 0.69-1.13, p=0.33). When stratified by TP53 mutation status, HR of HMA/VEN vs. HMAm was favorable for TP53 wild-type (HR: 0.47; 95%CI: 0.29-0.74) but not TP53-mutant pts (HR=0.96; 95%CI: 0.66-1.41). Adjusting for other variables in the model, HR for pts who underwent vs. those who did not undergo allo-SCT were 0.65 (95% CI: 0.49-0.85) and 0.36 (95%CI: 0.24-0.53) in TP53 wild-type and mutant patients, respectively. Conclusion: In this large, international retrospective analysis from the icMDS VALIDATE database, HMA/VEN was associated with higher cCR rates—but not CR rates—compared to HMAm among pts with HR-MDS, though we observed no significant differences in OS. In our analysis, clinical benefit from the addition of VEN was most clear in TP53 wild-type pts, and allo-SCT was associated with improved OS regardless of baseline TP53 status. Our analysis was limited by the relatively small number of HMA/VEN-treated pts and heterogeneous real-world treatment patterns.
Clinical implications of TP53 mutations (TP53MT) in patients (pts) with higher risk Myelodysplastic Syndromes (HR-MDS) treated with hypomethylating agents (HMA) and allogeneic hematopoietic transplantation (allo-HCT): An analysis from the international con
Bláha, Ondřej , Ali, Najla Al , Stein, Eytan M. , Brunner, Andrew M. , McMahon, Christine M. , Shallis, Rory M. , Chandhok, Namrata S. , Logothetis, Constantine , Bidikian, Aram, Getz, Theodore, Harris, Amyah, Hawkins, Hayley, Ball, Somedeb , Grenet, Justin , Haferlach, Torsten , Maciejewski, Jaroslaw P. , Al-Rabi, Kamal , Halahleh, Khalid , Pleyer, Lisa , Pappa, Vassiliki, Consagra, Angela , Al‐Kali, Aref , Stahl, Maximilian , Sallman, David A. , Kewan, Tariq Zuheir , Bewersdorf, Jan Philipp , Lanino, Luca , Stempel, Jessica M. , Dezern, Amy Elizabeth , Sekeres, Mikkael A. , Uy, Geoffrey L. , Urrutia, Samuel , Carraway, Hetty E. , Desai, Pinkal , Griffiths, Elizabeth A. , Zeidner, Joshua F. , Savona, Michael R. , Roboz, Gail J. , Rolles, Benjamin , Wang, Eunice S. , Amaya, Maria L. , Xie, Zhuoer , Madanat, Yazan F. , Abaza, Yasmin , Badar, Talha , Campos, Jaclynn, Enjeti, Anoop Kumar , Hiwase, Devendra , Díez‐Campelo, María , Valcárcel, David , Haferlach, Claudia , Kotsianidis, Ιoannis , Pappa, Vasiliki , Santini, Valeria , Ogawa, Seishi , Nannya, Yasuhito , Komrokji, Rami S. , Porta, Matteo Giovanni Della , Zeidan, Amer M.

Mayo Clinic

Blood | December 4, 2025 | Volume: 146 | Issue: Supplement 1 | Pages: 3863-3863

10.1182/blood-2025-3863 Get It

Abstract Introduction TP53MT are associated with poor outcomes in MDS, especially in the context of biallelic MT. We have previously reported on outcomes of pts with HR-MDS with TP53MT who received HMA in the VALIDATE dataset (Kewan T et al, ASH 2023). Here we provide expanded analyses focusing on outcomes post allo-HCT, and we explore the prognostic significance of different classification methods for biallelic TP53MT. Methods The VALIDATE database includes 4,732 pts with MDS who received HMA-based frontline therapy from 32 international centers in 9 countries. For this study, only pts with HR-MDS with molecular data at time of diagnosis were included. Biallelic TP53MT status was assessed using three classification schemes: WHO 2022, ICC 2022, and a VAF-based Cleveland Clinic Foundation (CCF) method.1TP53 copy neutral loss of heterozygosity (CN-LOH) was evaluable in 386 pts (118 had TP53MT). Treatment responses were evaluated using IWG 2023 criteria (Zeidan A et al, Blood 2023). Composite complete remission (cCR) was defined as CR+CRbi+CRuni+CRh+CRequivalent. We calculated OS from time of HMA initiation to date of death or last follow up. Unsupervised clustering (MOSAIC framework) was applied to identify molecular subgroups within the TP53MT cohort. The study was funded by an independent grant from Abbvie. Results A total of 1,485 pts were included. Median age was 69 years (IQR: 62–76), with 66% male pts. Median bone marrow blast was 7%, and 28% had a complex karyotype. Treatment regimens included azacitidine (68%), decitabine (15%), HMA/Venetoclax (8%), and other HMA combinations (9%); 34% underwent allo-HCT. Overall, 392 (26%) had TP53MT with 430 TP53 mutations (missense: 316; truncating: 89). Biallelic TP53MT % varied by classification: 72% (WHO), 84% (ICC), and 85% (CCF). Compared to TP53 wild-type (TP53WT) pts, pts with TP53MT had worse OS (median: 11.5 vs. 23.9 months [mo], p< 0.001), were younger (68 vs. 70 years, p=0.039), and had lower counts at diagnosis. Complex karyotype (81% vs. 14%) and chromosomal abnormalities were more frequent in TP53MT pts. Pts with TP53MT also had fewer co-mutations in other genes. Response to HMA was evaluable in 1,094 pts: cCR and CR were 32% and 13%, respectively. TP53MT pts had higher cCR (39% vs. 29%, p=0.001) than TP53WT, but similar CR rates (16% vs. 12%, p=0.093). According to WHO 2022, biallelic TP53MT had higher CR rates than monoallelic TP53MT (18% vs. 8%, p=0.03), but similar cCR. ICC and CCF classifications did not differentiate response rates. Median OS did not differ by TP53MT allelic status using WHO or ICC definitions. However, using the CCF method, pts with biallelic TP53MT had shorter OS than monoallelic TP53MT (10.4 vs. 17.2 mo, p=0.038). In multivariable models adjusted for age, gender, and allo-HCT, only the CCF-defined biallelic TP53MT group had significantly worse OS (HR: 1.6; 95% CI: 1.1–2.4). TP53MT pts undergoing allo-HCT had improved OS regardless of allelic status. Median OS for TP53MT pts with allo-HCT was 18.9 vs. 9.2 mo without all-HCT. This benefit was observed across WHO, ICC, and CCF classifications. However, a TP53MT VAF ≥19% predicted worse OS even post allo-HCT (14.6 vs. 47.1 mo, p<0.001). At 1 year, the survival rate was 78% (95%CI: 69-89%) in TP53MT pts who underwent allo-HCT and had cCR vs. 68% (95%CI: 55-84%) in pts who did not have cCR. However, 1 year survival rate was significantly higher for pts with TP53MT who did not have allo-HCT and achieved cCR (60%, 95%CI: 48-76%) vs. no cCR (26%, 95%CI: 20-35%). Unsupervised clustering of 335 TP53MT pts identified 9 molecular clusters (MCs). MC2, characterized by low TP53MT VAF (median 17%), fewer co-mutations, and frequent del17p, was associated with significantly improved OS (17.9 mo) and predicted favorable outcome (HR for death: 0.6; 95% CI: 0.4–0.8). Other clusters were enriched for adverse features (e.g., high VAF, multi-hit TP53MT).Conclusions The CCF method appears to best classify biallelic TP53MT pts with worse survival in the absence of accurate assessment of LOH status. Treatment response per IWG 2023 for TP53MT pts was associated with OS only in non-transplanted pts. Allo-HCT improved survival across TP53MT subsets, but TP53 VAF ≥19% at diagnosis remained a strong negative prognostic factor. Integrative clustering revealed a less aggresive molecular subset among TP53MT pts, suggesting refined risk stratification may guide therapy in this high-risk population. Ref: 1.Bahaj et al. J Hematol Oncol 2023.
The prognostic significance (or lack) of achieving marrow complete remission (mCR) with hypomethylating agent-based therapy in patients with myelodysplastic syndrome
Bláha, Ondřej , Ali, Najla Al , Stein, Eytan M. , Brunner, Andrew M. , McMahon, Christine M. , Shallis, Rory M. , Chandhok, Namrata S. , Logothetis, Constantine , Bidikian, Aram, Getz, Theodore, Amaya, Maria , Hawkins, Hayley, Ball, Somedeb , Grenet, Justin , Haferlach, Torsten , Maciejewski, Jaroslaw P. , Sallman, David A. , Al-Rabi, Kamal , Halahleh, Khalid , Pleyer, Lisa , Pappa, Vassiliki, Consagra, Angela , Al‐Kali, Aref , Stahl, Maximilian , Rolles, Benjamin , Bewersdorf, Jan Philipp , Kewan, Tariq Zuheir , Stempel, Jessica M. , Lanino, Luca , Dezern, Amy Elizabeth , Sekeres, Mikkael A. , Uy, Geoffrey L. , Urrutia, Samuel , Carraway, Hetty E. , Desai, Pinkal , Griffiths, Elizabeth A. , Zeidner, Joshua F. , Savona, Michael R. , Roboz, Gail J. , Wang, Eunice S. , Xie, Zhuoer , Madanat, Yazan F. , Abaza, Yasmin , Badar, Talha , Campos, Jaclynn, Enjeti, Anoop Kumar , Hiwase, Devendra , Díez‐Campelo, María , Valcárcel, David , Haferlach, Claudia , Kotsianidis, Ιoannis , Pappa, Vasiliki , Santini, Valeria , Ogawa, Seishi , Nannya, Yasuhito , Della Porta, Matteo Giovanni , Komrokji, Rami S. , Zeidan, Amer M.

Mayo Clinic

Blood | December 4, 2025 | Volume: 146 | Issue: Supplement 1 | Pages: 3865-3865

10.1182/blood-2025-3865 Get It

Abstract Introduction: Marrow complete remission (mCR) in 2006 IWG criteria for MDS (Cheson B et al, Blood 2006) reflects achieving bone marrow (BM) blast percentage below 5% but is frequently not associated with meaningful count recovery. While mCR + hematologic improvement (HI) does reflect wide ranges of count improvement or transfusion reductions, HI is difficult to measure accurately in routine clinical practice. The 2023 International Working Group (IWG) response criteria (Zeidan A et al, Blood 2023) eliminated the mCR category without meaningful count recovery and reclassified mCR associated with meaningful count recovery into specific “less-than-CR” categories. Still, many clinical trials continue to use mCR as a secondary efficacy endpoint or as a part of overall response rate (ORR). Within the icMDS VALIDATE database, we assessed the association of mCR with OS in hypomethylating agent (HMA)-treated higher risk (HR)-MDS patients among both (1) transplanted and (2) non-transplanted patients. Methods We included patients with HR-MDS (defined as IPSS ≥1.5 and/or IPSS-R >3.5) who received HMA-based therapies from the international icMDS VALIDATE dataset. We evaluated the best response by IWG 2006 criteria into CR, mCR, or no CR/mCR. We then reclassified patients with mCR per IWG 2023 criteria into either (A) having achieved a composite CR (cCR) defined as CR + CR equivalent (CRequ) + CR with bilineage count recovery (CRbi) + CR with unilineage count recovery (CRuni) + CR with partial hematologic recovery (CRh) or (B) not having achieved cCR (no cCR). OS was calculated from time of HMA initiation to date of death or last follow-up by using 6-month landmark analyses. We used Kaplan-Meier methods to estimate OS, and the Log-rank test to compare OS. VALIDATE is supported by an independent grant from AbbVie. Results A total of1049 patients met eligibility.Median age of patients was 69 (range 21-95), 64% were men. While 61% received azacitidine, 17% received decitabine, and 22% received HMA-based combination therapy. In total, 37% underwent subsequent allogenic stem cell transplantation (allo-HCT). Based on IWG 2006 criteria, 17%, 33%, and 50% achieved CR, mCR, and no CR/mCR as their best response, respectively. Patients achieving CR had superior median OS (25 months, 95% CI: 21-34 months) compared to those with mCR (16 months, 95% CI: 13-18 months; p=0.038) and no CR/mCR (15 months, 95% CI: 12-17 months; p=0.001). In patients who received a subsequent allo-HCT, the median OS for patients with mCR (30 months, 95% CI: 21-54 months; 1 year OS: 71%, 2 year OS: 55%) did not significantly differ compared to patients with CR (59 months, 95% CI: 25 months-not reached, p=0.80; 1 year OS: 73%, 2 year OS 62%) and patients with no CR/mCR (32 months, 95% CI: 21-45 months, p=0.46; 1 year OS: 69%, 2 year OS 54%). In contrast, in patients treated with HMA therapy alone without subsequent allo-HCT, median OS for patients with mCR (11 months, 95% CI: 9-15 months; 1 year OS: 46%, 2 year OS: 23%) did not significantly differ compared to patients with no CR/mCR (11 months, 95% CI: 9-14 months, p=0.85; 1 year OS: 47%, 2 year OS: 22%) but was significantly shorter compared to patients with CR (20 months, 95% CI: 17-28 months, p<0.001; 1 year OS: 69%, 2 year OS: 46%). Patients with mCR by IWG 2006 (N=347) were reclassified per IWG 2023 into having either achieved a cCR (N=219, 63%) or no cCR (N=128, 37%). Specifically, patients with mCR were reclassified per IWG 2023 into CR (4.9%), CRequ (0.6%), CRbi (26.8%), CRuni (29.4%), CRh (1.4%), PR (0%), HI (10%), no response (21.9%) and PD (4.9%). Patients with mCR who were reclassified into cCR had an improved median OS (16 months, 95% CI: 15-26 months; 1 year OS: 62%; 2 year OS: 43%) compared to patients reclassified into no cCR per IWG 2023 (13 months, 95% CI: 11-17 months, p=0.023; 1 year OS: 52%; 2 year OS: 31%). Conclusions Using the large icMDS VALIDATE dataset, we found that achievement of mCR by 2006 IWG criteria was not associated with improved OS compared to patients who did not achieve CR/mCR. Reclassification of mCR using IWG 2023 highlights the heterogeneity within the mCR group and suggests that IWG 2023 criteria stratifies outcomes in patients previously labeled as mCR by IWG 2006. IWG 2023 should be the standard used for ORR assessment in all future clinical trials involving patients with HR-MDS.
Discovery of a MET-driven monogenic cause of steatotic liver disease
Wagenknecht, Jessica B. , Jorge, Salomão Dória , Tian, Shulan , Luehrs, Anthony C. , Assuncao, Thiago M. de , Cao, Yang , Klee, Eric W. , Vairo, Filippo , Urrutia, Raúl , Vairo, Filippo Pinto e , Zimmermann, Michael T. , Vierkant, Robert A. , Mathison, Angela , Atwal, Paldeep S , Allen, Alina M. , Lazaridis, Konstantinos N.

Mayo Clinic

Hepatology | January 29, 2025 | Volume: 82 | Issue: 6 | Pages: 1512-1522

10.1097/hep.0000000000001249 | PMID 39879586 Get It

Background and Aims: Metabolic dysfunction–associated steatotic liver disease affects about a third of adults worldwide and is projected soon to be the leading cause of liver cirrhosis. It occurs when fat accumulates in hepatocytes and can progress to metabolic dysfunction–associated steatohepatitis, liver cirrhosis, and HCC. Metabolic dysfunction–associated steatotic liver disease pathogenesis is believed to involve a combination of genetic and environmental risk factors. Single nucleotide polymorphisms have been implicated, but non-syndromic monogenic causes are lacking. Approach and Results: We identified a novel genetic variant in a familial case of metabolic dysfunction–associated steatohepatitis and performed deep variant functional analysis, including protein modeling, dynamics, and cell-based assays to assess molecular mechanisms of dysfunction and altered cellular signaling. We analyzed exome sequencing data of 3904 individuals with steatotic liver disease (SLD) to identify additional cases and establish the link between specific gene variants and SLD diagnosis. We discovered and functionally validated the NM_000245.4:c.3505A>T; p.(Ile1169Phe) variant in the MET (mesenchymal-epithelial transition) kinase domain as a monogenic cause of SLD. Subsequently, we detected additional ultra-rare, previously uninterpreted, and likely deleterious variants in MET from screening sequencing data. Among individuals with confirmed SLD based on electronic record review, 1.1% (45/3904) had rare predicted deleterious MET variants. Eight of 45 (17.7%) individuals had predicted deleterious variants in the MET kinase domain confirmed to be functionally like the familial case variant. Conclusions: We report the first germline nonmalignant rare MET -driven disease, a monogenic form of SLD.
Targeting the Epigenetic Regulator CBX5 Promotes Fibroblast Metabolic Reprogramming and Inhibits Lung Fibrosis
Hong, Jeongmin , Pham, Tho X., Nicolas, K., Sharov, Andrey A. , Meridew, Jeffrey A., Lomberk, Gwen , Huang, Steven K. , Ligresti, Giovanni , Huang, Steven K , Ligresti, Giovanni , Lomberk, Gwen L , Lee, Jisu , Raslan, Ahmed , Urrutia, Raúl

Mayo Clinic

American Journal of Respiratory Cell and Molecular Biology | December 6, 2024 | Volume: 72 | Issue: 6 | Pages: 627-642

10.1165/rcmb.2024-0255oc | PMID 39642371 Get It

Abstract Idiopathic pulmonary fibrosis (IPF) is characterized by the sustained activation of interstitial fibroblasts leading to excessive collagen deposition and progressive organ failure. Epigenetic and metabolic abnormalities have been shown to contribute to the persistent activated state of scar-forming fibroblasts. However, how epigenetic changes regulate fibroblast metabolic responses to promote fibroblast activation and progressive fibrosis remains largely unknown. Here, we show that the epigenetic regulator CBX5 (chromobox protein homolog 5) is critical to the transition of quiescent fibroblasts to activated collagen-producing fibroblasts in response to bleomycin-induced lung injury. Loss of mesenchymal CBX5 attenuated fibrosis development, and this effect was accompanied by the downregulation of pathogenic fibroblast genes, including Cthrc1, Col1a1, and Spp1, and by the upregulation of metabolic genes with antifibrotic activity such as Ppara and Pparg. Single-cell RNA sequencing and immunohistochemistry analyses revealed that CBX5 expression was enriched in pathogenic fibroblasts and fibroblastic foci of IPF lungs. Bulk RNA-sequencing analysis combined with metabolic assessments demonstrated that CBX5 silencing in IPF fibroblasts potently inhibited transforming growth factor–stimulated glycolysis while enhancing AMPK signaling and mitochondrial metabolism. Finally, interruption of the CBX5 pathway in IPF fibroblasts in vitro and in IPF lung explants ex vivo synergistically potentiated the activation of metformin-induced AMP-activated protein kinase activation and inhibited collagen secretion. Collectively, our findings identify CBX5 as an epigenetic regulator linking metabolic maladaptation to the persistent activated state of lung fibroblasts during IPF progression.
Structural and Dynamic Analyses of Pathogenic Variants in PIK3R1 Reveal a Shared Mechanism Associated among Cancer, Undergrowth, and Overgrowth Syndromes
Dsouza, Nikita R., Cottrell, Catherine E. , Davies, Olivia M. T. , Tollefson, Megha M. , Frieden, Ilona J. , Basel, Donald , Drolet, Beth A. , Urrutia, Raúl , Zimmermann, Michael T.

Mayo Clinic

Life | February 23, 2024 | Volume: 14 | Issue: 3 | Pages: 297

10.3390/life14030297 | PMID 38541623 Get It

The PI3K enzymes modify phospholipids to regulate cell growth and differentiation. Somatic variants in PI3K are recurrent in cancer and drive a proliferative phenotype. Somatic mosaicism of PIK3R1 and PIK3CA are associated with vascular anomalies and overgrowth syndromes. Germline PIK3R1 variants are associated with varying phenotypes, including immunodeficiency or facial dysmorphism with growth delay, lipoatrophy, and insulin resistance associated with SHORT syndrome. There has been limited study of the molecular mechanism to unify our understanding of how variants in PIK3R1 drive both undergrowth and overgrowth phenotypes. Thus, we compiled genomic variants from cancer and rare vascular anomalies and sought to interpret their effects using an unbiased physics-based simulation approach for the protein complex. We applied molecular dynamics simulations to mechanistically understand how genetic variants affect PIK3R1 and its interactions with PIK3CA. Notably, iSH2 genetic variants associated with undergrowth destabilize molecular interactions with the PIK3CA receptor binding domain in simulations, which is expected to decrease activity. On the other hand, overgrowth and cancer variants lead to loss of inhibitory interactions in simulations, which is expected to increase activity. We find that all disease variants display dysfunctions on either structural characteristics or intermolecular interaction energy. Thus, this comprehensive characterization of novel mosaic somatic variants associated with two opposing phenotypes has mechanistic importance and biomedical relevance and may aid in future therapeutic developments.
Dissecting the Role of EZH2 and H3K27me3 in Endometriosis
Colón-Caraballo, Mariano, Soto-Vargas, John Lee , Urrutia, Raúl , Flores, Idhaliz

Mayo Clinic

The FASEB Journal | November 26, 2023 | Volume: 31 | Issue: S1 | Pages: No page available

10.1096/fasebj.31.1_supplement.1058.1 Get It

Background Endometriosis, defined as the growth and development of endometrial like tissue, ( i.e., glands and stroma) outside the uterine cavity, is a gynecological condition that affects 10% of women in their reproductive age. Cumulative evidence has demonstrated that candidate genes which are related with cellular behaviors characteristic of endometriosis are epigenetically regulated by DNA methylation and histone acetylation. However, the specific role of histone methylation and the enzymes responsible for setting these histone marks ( e.g., histone methyltransferases‐HMT's) in the regulation of these candidate genes is still unknown. EZH2 is an HMT that sets the H3K27me3 histone mark, a repressor of the transcriptional machinery. We have previously reported that endometriotic lesions are characterized by high levels of H3K27me3; therefore, we aimed to assess basal and hormone‐regulated protein expression levels of EZH2 isoforms (α and β) and also elucidate if H3K27me3 is enriched within or near promoter regions of candidate genes. Methods Western Blot (WB) was performed to determine basal and ovarian steroid EZH2 protein levels in cell lines. Immunohistochemistry (IHC) of an endometriosis‐TMA was used to assess EZH2 α and β protein levels in tissue samples. Chromatin immunoprecipitation (ChIP‐qPCR) with an H3K27me3 antibody was conducted using endometrial and endometriotic samples. Scratch Assay was performed to determine the effect of EZH2 inhibition on proliferative cellular behavior Results WB results suggest that endometriotic cells expressed higher levels of EZH2α, compared to non‐endometriotic cells. Also, hormonal treatments did not modulate EZH2 isoform expression in any of the cell lines tested. IHC indicated that in endometriotic lesions the glands and stroma had higher EZH2α and β protein levels compared to eutopic endometrium from patients. ChIP‐qPCR results showed higher levels of H3K27me3 levels within promoter regions of candidate genes in at least some of the endometriotic lesions. Pharmacological inhibition of EZH2 reduced the proliferative rate of the endometriotic cells. Conclusions The present study is the first in reporting that EZH2 isoform protein expression is elevated in endometriosis but not regulated by steroid hormones. We also showed that H3K27me3 is elevated in the promoter region of candidate genes in some lesions. Elucidating the expression profile and function of HMTs may support the use of novel histone methyltransferases inhibitors (HMTi) as a possible treatment for this enigmatic disease. Support or Funding Information R01HD050509, NCI1U56CA126379‐01, R25GM082406.
Writers and readers of H3K9me2 form distinct protein networks during the cell cycle that include candidates for H3K9 mimicry
Pollin, Gareth , Assuncao, Thiago M. de , Jorge, Salomão Dória , Chi, Young‐In , Charlesworth, M. Cristine , Lomberk, Gwen , Lomberk, Gwen L , Charlesworth, M. Cristine , Madden, Benjamin J. , Iovanna, Juan , Zimmermann, Michael T. , Urrutia, Raúl

Mayo Clinic

Bioscience Reports | October 2, 2023 | Volume: 43 | Issue: 10 | Pages: No page available

10.1042/bsr20231093 | PMID 37782747 Get It

Abstract Histone H3 lysine 9 methylation (H3K9me), which is written by the Euchromatic Histone Lysine Methyltransferases EHMT1 and EHMT2 and read by the heterochromatin protein 1 (HP1) chromobox (CBX) protein family, is dysregulated in many types of cancers. Approaches to inhibit regulators of this pathway are currently being evaluated for therapeutic purposes. Thus, knowledge of the complexes supporting the function of these writers and readers during the process of cell proliferation is critical for our understanding of their role in carcinogenesis. Here, we immunopurified each of these proteins and used mass spectrometry to define their associated non-histone proteins, individually and at two different phases of the cell cycle, namely G1/S and G2/M. Our findings identify novel binding proteins for these writers and readers, as well as corroborate known interactors, to show the formation of distinct protein complex networks in a cell cycle phase-specific manner. Furthermore, there is an organizational switch between cell cycle phases for interactions among specific writer–reader pairs. Through a multi-tiered bioinformatics-based approach, we reveal that many interacting proteins exhibit histone mimicry, based on an H3K9-like linear motif. Gene ontology analyses, pathway enrichment, and network reconstruction inferred that these comprehensive EHMT and CBX-associated interacting protein networks participate in various functions, including transcription, DNA repair, splicing, and membrane disassembly. Combined, our data reveals novel complexes that provide insight into key functions of cell cycle-associated epigenomic processes that are highly relevant for better understanding these chromatin-modifying proteins during cell cycle and carcinogenesis.