Martina Sarchi
@unipv.it
University of Pavia
Scopus Publications
- Loss of function of the chromatin remodeling gene INO80D leads to neurogenic features of schizophrenia
Anna B. Sunshine, Suleyman Gulsuner, C. Andrew Williams, Martina Sarchi, Robert Y. Chen, et al.
Proceedings of the National Academy of Sciences of the United States of America, 2026
Schizophrenia has been linked to severely damaging de novo mutations in synaptic junction proteins, neurotransmitter receptors, transcription factors, and chromatin remodeling proteins. In a patient with schizophrenia in the absence of a family history of severe mental illness, we identified de novo nonsense mutation, INO80D p.Q568X, associated with both a truncated protein and partial nonsense-mediated decay. Three experiments were undertaken to evaluate the consequences of the mutation. 1) In neural stem cells (iNSCs) differentiated from WTC11 iPSCs, CRISPRi knockdown of INO80D led to downregulation of three subunits of the AMPA-glutamate receptor, of multiple genes mutant in schizophrenia, and of genes of synaptic function. 2) INO80D p.Q568X iNSCs and neurons differentiated from patient-derived induced pluripotent stem cells (iPSCs) had significantly lower expression of neurogenesis genes compared to patient-derived cells with the mutation corrected by CRISPR-Cas9 gene editing. Patient-derived INO80D p.Q568X neurons had significantly higher expression of cell division genes compared to lines with the mutation corrected, consistent with the possibility that some of these cells may be undergoing mitosis, which is not normal for neurons. 3) Finally, on microelectrode array (MEA) plates, WTC11-derived glutamatergic neurons with reduced expression of INO80D had more rapid firing rate and increased average network burst duration, both features of neurons derived from patients with neurodevelopmental disorders. Overall, these findings suggest that partial loss of INO80D function due to de novo mutation may have disrupted normal neurodevelopment and contributed to the schizophrenia of this patient. - TGF-Β PATHWAY DEREGULATION IN SF3B1 MUTATED LOW RISK MYELODYSPLASTIC SYNDROME PATIENTS
Eleonora Lumia
Haematologica, 2026
Introduction. Myelodysplastic syndromes (MDS) associated with mutations in genes belonging to the splicing machinery, such as SF3B1, SRSF2, U2AF1 and ZRSR2, are characterized by inefficient hematopoiesis and variable risk of evolving into AML. Mutations affecting SF3B1 are among the most common alterations, correlating with low-risk phenotype (LR-MDS) and response to Luspatercept treatment. We were interested in the characterization of the expression profiles and the spliceosome of LR-MDS mutated for splicing factors (SF). Methods: We selected a study cohort of 50 LR-MDS (30 M and 20 F, med. age 75 yrs, range 40-91) characterized by mutations in SF genes (SF3B1=15, SRSF2=9, U2AF1=11 and SF-wt=15).Results. RNA-Seq on 50 LR-MDS vs 64 non-haematologic pts revealed 4221 differentially expressed genes (DEGs), 3921 down- and 300 up-regulated. When subgrouping patients according to specific SF mutations, SF3B1-mutated MDS (n=15) showed the highest number of DEGs (622: 10 down- and 612 up-regulated) when compared to SF-wt pts (n=7). Gene Ontology analysis identified 37 deregulated pathways in SF3B1-mut vs SF-wt pts. We found 6 DEGs in TGF-β pathway (CHRD, DCN, SMAD9, FST, ID4, PITX2) and 10 in TGF-β modulators (BDNF, BMPER, COL1A1, COL1A2, FN1, GLI2, IGF1, MMP2, NFIB and PLAU). DEGs were confirmed using Q-rt-PCR assays: DCN (p=0,004), FST (p=0,017), SMAD9 (p=0,030), FN1 (p=0,004), IGF1 (p=0,030) and MMP2 (p= 0,004). We then investigated the presence of alternative splicing events (ASE) within the TGF-β pathway, identifying an intron 15 retention on the USP15 gene, a ubiquitin specific protease. This yields a truncated protein isoform (USP15-TR), which was preferentially expressed in SF3B1-K700E vs wt MDS, without changes in total mRNA. USP15-TR was overexpressed in SF3B1-K700E mutated K562 cells (p<0.02) as compared to USP15 full length (USP15-FL), without changes in total mRNA.The stability of USP15-TR was confirmed in K562 SF3B1-K700E cells by non-sense mediated decay assays using cycloheximide. Western blot (WB) analysis confirmed a reduction of USP15-FL protein, with a relative increase of USP15-TR (p<0.05). Looking for alterations in protein expression and phosphorylation of TGF-β pathway players, bioinformatic analysis in MDS samples showed reduction of SMAD3 and SMAD7 mRNA expression, confirmed at protein level (WB) in the K562 SF3B1-K700E cell model (p<0.01 and p<0.05). SMAD2 protein levels were slightly reduced, while phosphorylation was clearly increased, highlighting hyperactivation of the TGF-β pathway in SF3B1-mut cells. This was also confirmed by the ectopic expression of either USP15 isoforms in HEK293T cell, showing an increased SMAD2 phosphorylation in USP15-TR vs USP15-FL engineered cells.Conclusions. Our preliminary studies highlight the deregulation of TGF-β pathway at mRNA, ASE and protein levels in SF3B1-mut pts and engineered cells, suggesting the potential role of USP15 as biomarker and/or actional target in clinical practice. - Evolutionary trajectories of myelodysplastic syndromes/neoplasms
Maria Creignou, Martina Sarchi, Elsa Bernard, Luca Malcovati
Seminars in Cancer Biology, 2026 - A vertically integrated system for tracking and assessing cell-cycle-aware phenotypes under confinement
Melissa Pezzotti, Eloisa Torchia, Julius Zimmermann, Sara Rigolli, Alessandro Enrico, et al.
APL Bioengineering, 2026
Quantitative cell biology often examines migration and cell-cycle (CC) progression separately, limiting insights into their interplay under spatial constraints. Here, we present a vertically integrated platform combining multiplexed fluorescent reporters for CC phases, actin, and tubulin with photopatterned extracellular matrix islands of defined sizes, alongside an automated imaging pipeline (Fab2Mic) for high-throughput, live-cell tracking of migration and CC dynamics under planar confinement. Using HT1080 fibrosarcoma cells, we observed that planar confinement progressively reduced cell area and cytoskeletal spread, altered CC phase distributions, and increased abnormal CC events, including prolonged G1 and mitotic slippage, which is unique to confined conditions. Dynamic imaging revealed CC-dependent motility variations, with faster migration in G1. This system enables systematic, CC-aware mechanobiology studies under controlled confinement, providing access to dynamic phenotypes inaccessible to static assays and offering a scalable approach for mechanistic investigations and screening applications. - A precision medicine approach to the myelodysplastic syndrome with isolated deletion 5q, 50 years after its discovery
Marco Roncador, Elsa Bernard, Robert P Hasserjian, Jacqueline Boultwood, Chiara Elena, et al.
Blood, 2025
In 1974, Vanden Berghe et al described a distinct hematologic disorder associated with acquired, interstitial deletion of part of the long arm of chromosome 5. This condition is now classified as myelodysplastic syndrome (MDS) with isolated deletion 5q, or MDS-del(5q). The common deletion region 5q32-5q33 contains several genes and microRNAs whose expression levels are reduced in hematopoietic cells, consistent with the loss of one allele. Haploinsufficiency production of multiple gene transcripts, primarily involving CSNK1A1, RPS14, MIR145, and MIR146A, results in myelodysplastic hematopoiesis. Lenalidomide can selectively suppress the del(5q)-mutant clone by promoting proteasomal degradation of casein kinase 1A1 and inducing mutant stem cell failure. However, lenalidomide is not a curative treatment, as almost all patients relapse. Molecular profiling studies have significantly improved our understanding of MDS-del(5q). Only a minority of patients have interstitial deletion 5q as their sole genetic lesion, a condition that is associated with an indolent clinical course. Most patients have co-occurring somatic mutations in myeloid genes, including DNMT3A, TET2, ASXL1, SF3B1, TP53, RUNX1, and CSNK1A1. These comutations have independent effects on leukemic transformation and survival, so genomic profiling is required for implementing a precision management approach to MDS-del(5q) in a clinical setting. Accurate assessment of the TP53 allelic state is crucial for distinguishing MDS-del(5q) from TP53-mutant MDS, a myeloid malignancy characterized by TP53 multihit state and very aggressive clinical course. Genomic profiling is also critical for therapeutic decision making in patients with MDS-del(5q), particularly for assessing a patient's eligibility for allogeneic transplantation, which remains the only curative treatment. - Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes
Martina Sarchi, Courtnee A. Clough, Anna Gallì, Cristina Picone, Beatrice Ferrari, et al.
Blood Advances, 2025
Myelodysplastic syndromes (MDS) are clonal stem cell disorders driven by heterogeneous genetic alterations leading to variable clinical course. MDS with splicing factor SF3B1 mutations is a distinct subtype with a favorable outcome. However, selected comutations induce poor prognosis and how these genetic lesions cooperate in human hematopoietic stem and progenitor cells (HSPCs) during disease progression is still unclear. Here, we integrated clinical and molecular profiling of patients with SF3B1 mutations with gene editing of primary and induced pluripotent stem cell–derived human HSPCs to show that high-risk comutations impart distinct effects on lineage programs of SF3B1-mutant HSPCs. Secondary RUNX1 or STAG2 mutations were clinically associated with advanced disease and reduced survival. However, RUNX1 and STAG2 mutations induced opposing regulation of myeloid transcriptional programs and differentiation in SF3B1-mutant HSPCs. Moreover, high-risk RUNX1 and STAG2, but not low-risk TET2, mutations expanded distinct SF3B1-mutant HSPC subpopulations. These findings provide evidence that progression from low- to high-risk MDS involves distinct molecular and cellular routes depending on comutation patterns. - Understanding Human Oncogene Function and Cooperativity in Myeloid Malignancy Using iPSCs
Martina Sarchi, Sergei Doulatov
Experimental Hematology, 2025 - Mis-splicing of Mitotic Regulators Sensitizes SF3B1-Mutated Human HSCs to CHK1 Inhibition
Martina Sarchi, Courtnee A. Clough, Edie I. Crosse, Jason Kim, Laura D. Baquero Galvis, et al.
Blood Cancer Discovery, 2024
Splicing factor SF3B1 mutations are frequent somatic lesions in myeloid neoplasms that transform hematopoietic stem cells (HSCs) by inducing mis-splicing of target genes. However, the molecular and functional consequences of SF3B1 mutations in human HSCs and progenitors (HSPCs) remain unclear. Here, we identify the mis-splicing program in human HSPCs as a targetable vulnerability by precise gene editing of SF3B1 K700E mutations in primary CD34+ cells. Mutant SF3B1 induced pervasive mis-splicing and reduced expression of genes regulating mitosis and genome maintenance leading to altered differentiation, delayed G2/M progression, and profound sensitivity to CHK1 inhibition (CHK1i). Mis-splicing or reduced expression of mitotic regulators BUBR1 and CDC27 delayed G2/M transit and promoted CHK1i sensitivity. Clinical CHK1i prexasertib selectively targeted SF3B1-mutant immunophenotypic HSCs and abrogated engraftment in vivo. These findings identify mis-splicing of mitotic regulators in SF3B1-mutant HSPCs as a targetable vulnerability engaged by pharmacological CHK1 inhibition. Significance: In this study, we engineer precise SF3B1 mutations in human HSPCs and identify CHK1 inhibition as a selective vulnerability promoted by mis-splicing of mitotic regulators. These findings uncover the mis-splicing program induced by mutant SF3B1 in human HSPCs and show that it can be therapeutically targeted by clinical CHK1 inhibitors. - GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies
Salima Benbarche, Jose Mario Bello Pineda, Laura Baquero Galvis, Jeetayu Biswas, Bo Liu, et al.
Molecular Cell, 2024 - R-Loop Accumulation in Spliceosome Mutant Leukemias Confers Sensitivity to PARP1 Inhibition by Triggering Transcription–Replication Conflicts
Zhiyan Silvia Liu, Sayantani Sinha, Maxwell Bannister, Axia Song, Erica Arriaga-Gomez, et al.
Cancer Research, 2024
RNA splicing factor (SF) gene mutations are commonly observed in patients with myeloid malignancies. Here we showed that SRSF2- and U2AF1-mutant leukemias are preferentially sensitive to PARP inhibitors (PARPi), despite being proficient in homologous recombination repair. Instead, SF-mutant leukemias exhibited R-loop accumulation that elicited an R-loop–associated PARP1 response, rendering cells dependent on PARP1 activity for survival. Consequently, PARPi induced DNA damage and cell death in SF-mutant leukemias in an R-loop-dependent manner. PARPi further increased aberrant R-loop levels, causing higher transcription–replication collisions and triggering ATR activation in SF-mutant leukemias. Ultimately, PARPi-induced DNA damage and cell death in SF-mutant leukemias could be enhanced by ATR inhibition. Finally, the level of PARP1 activity at R-loops correlated with PARPi sensitivity, suggesting that R-loop-associated PARP1 activity could be predictive of PARPi sensitivity in patients harboring SF gene mutations. This study highlights the potential of targeting different R-loop response pathways caused by spliceosome gene mutations as a therapeutic strategy for treating cancer. Significance: Spliceosome-mutant leukemias accumulate R-loops and require PARP1 to resolve transcription–replication conflicts and genomic instability, providing rationale to repurpose FDA-approved PARP inhibitors for patients carrying spliceosome gene mutations. - Prevalence and clinical expression of germ line predisposition to myeloid neoplasms in adults with marrow hypocellularity
Elisabetta Molteni, Elisa Bono, Anna Gallì, Chiara Elena, Jacqueline Ferrari, et al.
Blood, 2023 - Coordinated missplicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome
Courtnee A. Clough, Joseph Pangallo, Martina Sarchi, Janine O. Ilagan, Khrystyna North, et al.
Blood, 2022 - Relationship between clone metrics and clinical outcome in clonal cytopenia
Anna Gallì, Gabriele Todisco, Eulalia Catamo, Cinzia Sala, Chiara Elena, et al.
Blood, 2021 - Co-mutation pattern, clonal hierarchy, and clone size concur to determine disease phenotype of SRSF2 P95-mutated neoplasms
Gabriele Todisco, Maria Creignou, Anna Gallì, Paola Guglielmelli, Elisa Rumi, et al.
Leukemia, 2021
