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Supplementary Table 2

Figures S1 to S17

Supplementary Table 1

An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. The commonality among SLC5A3-dependent AML lines is the transcriptional silencing of ISYNA1, which encodes the rate-limiting enzyme for myo-inositol biosynthesis, inositol-3-phosphate synthase 1. We use gain- and loss-of-function experiments to reveal a synthetic lethal genetic interaction between ISYNA1 and SLC5A3 in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation of ISYNA1 occur in a recurrent manner in human AML patient samples, in association with IDH1/IDH2 and CEBPA mutations. Our findings reveal myo-inositol as a nutrient dependency in AML caused by the aberrant silencing of a biosynthetic enzyme.Significance:We show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically defined subset of AML.This article is highlighted in the In This Issue feature, p. 275

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and phenocopies a muscle precursor that fails to undergo terminal differentiation. The alveolar subtype (ARMS) has the poorest prognosis and represents the greatest unmet medical need for RMS. Emerging evidence supports the role of epigenetic dysregulation in RMS. Here we show that SMARCA4/BRG1, an ATP-dependent chromatin remodeling enzyme of the SWI/SNF complex, is prominently expressed in primary tumors from ARMS patients and cell cultures. Our validation studies for a CRISPR screen of 400 epigenetic targets identified SMARCA4 as a unique factor for long-term (but not short-term) tumor cell survival in ARMS. A SMARCA4/SMARCA2 protein degrader (ACBI-1) demonstrated similar long-term tumor cell dependence in vitro and in vivo. These results credential SMARCA4 as a tumor cell dependency factor and a therapeutic target in ARMS.

An enhanced requirement for nutrients is a hallmark property of cancer cells. Here, we optimized an in vivo genetic screening strategy in acute myeloid leukemia (AML), which led to the identification of the myo-inositol transporter SLC5A3 as a dependency in this disease. We demonstrate that SLC5A3 is essential to support a myo-inositol auxotrophy in AML. The commonality among SLC5A3-dependent AML lines is the transcriptional silencing of ISYNA1, which encodes the rate-limiting enzyme for myo-inositol biosynthesis, inositol-3-phosphate synthase 1. We use gain- and loss-of-function experiments to reveal a synthetic lethal genetic interaction between ISYNA1 and SLC5A3 in AML, which function redundantly to sustain intracellular myo-inositol. Transcriptional silencing and DNA hypermethylation of ISYNA1 occur in a recurrent manner in human AML patient samples, in association with IDH1/IDH2 and CEBPA mutations. Our findings reveal myo-inositol as a nutrient dependency in AML caused by the aberrant silencing of a biosynthetic enzyme. Significance: We show how epigenetic silencing can provoke a nutrient dependency in AML by exploiting a synthetic lethality relationship between biosynthesis and transport of myo-inositol. Blocking the function of this solute carrier may have therapeutic potential in an epigenetically defined subset of AML. This article is highlighted in the In This Issue feature, p. 275

The introduction of immune-checkpoint inhibitors (ICPI) in recent years has changed the natural course of many neoplasms. However, patients receiving these medications may present immune-mediated adverse events; management includes temporary or permanent cessation of treatment and corticosteroids, occasionally combined with other immunomodulators. Such immunosuppression, however, also has numerous adverse events and even if it is effective in controlling toxicity, it delays immunotherapy reinitiation, as current evidence requires dose tapering to ≤10 mg prednisolone equivalent before rechallenge. Enteric-coated budesonide is a corticosteroid formulation acting primarily to the intestine and liver, as a result of its extensive first-pass hepatic metabolism.A 76-year-old woman treated with ipilimumab for metastatic melanoma presented with abdominal pain, vomiting, and diarrhea for at least the previous 4 days. Laboratory tests, among others, revealed elevated aminotransferases and C-reactive protein. During hospitalization, the patient also developed fever.The patient, after excluding alternative causes of aminotransferase elevation, was diagnosed with grade 3 ipilimumab-associated hepatotoxicity.Budesonide monotherapy was administered; initial daily dose was 12 mg.Fever subsided after the first dose of budesonide. Aminotransferases returned to normal-near normal approximately 1 month after the first dose of budesonide. After this point, daily dose was reduced by 3 mg every 2 weeks, with no clinical or biochemical relapse.This case of ICPI hepatitis is, to our knowledge, the first in the literature managed with budesonide monotherapy. Therefore, budesonide may be a potentially attractive option for the management of ICPI-associated liver injury in cases where corticosteroid treatment is necessary due to its safety profile and the potential advantage of faster immunotherapy rechallenge in selected patients without requiring dose tapering, in contrast to systemically acting corticosteroids. Clinical trials should be conducted in the future in order to validate or refute these findings.

Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

Native Americans domesticated maize (

Background: Atorvastatin reduces oxidized low-density lipoprotein (oxLDL) levels and reduces the rate of plaque progression in patients with and without prior carotid angioplasty. The aim of our study was to investigate the durability of this effect and to explore possible prognostic impact of oxLDL levels on carotid stenosis and plaque stability. Methods: 106 patients (71 males, mean age 64.82±7.26 years) were studied. They were divided into two groups. Group 1 including patients with carotid stenosis >70% (n=50) who underwent carotid angioplasty prior to enrolment. Group 2 included those with 70%) was noticed in four patients, yet no further intervention was needed due to plaque morphology (echo-grade IV). In group 2, carotid stenosis was initially reduced (6th month – 4th year) and later relapsed (5th – 10th year), yet plaque morphology was recorded as type III or IV in almost all patients of group 2 (53=95%), indicating a significantly lower risk for stroke. Conclusion: Atorvastatin treatment to a target of LDL

Background Mycobacterial infections can cause significant morbidity when cellular immunity is compromised. Patients with AIDS can be affected directly from infection or through mycobacterial IRIS, especially if they are previously untreated for HIV. Herein a case of tuberculous lymphadenitis is reported, which primarily responded to antimicrobials but complicated by IRIS and cat-scratch disease at a later course. Case presentation A 23-year-old man, intravenous drug user with untreated HIV and HCV infection presented with fever and painful cervical lymphadenopathy. Mycobacterium tuberculosis was isolated from PCR and culture of ultrasound-guided lymph node aspirate and a four-drug anti-TB regimen was subsequently administered, leading to complete resolution of clinical and laboratory abnormalities. Given the patient’s CD4 count (67 cells per mm3), antiretroviral treatment started seven weeks after TB treatment initiation. Within the first month of ART fever recurred along with cervical lymph node inflammation. Paradoxical IRIS was considered as the most probable diagnosis but workup expanded, revealing acute Bartonella infection. A posteriori, the patient remembered being scratched by a stray cat two weeks before his new symptoms started. Doxycycline and corticosteroid monotherapy failed to resolve symptoms, whereas a combination of doxycycline for 3 months and methylprednisolone with long-term tapering led to negative follow-up Bartonella antibodies and complete clinical and biochemical response, without recurrence. Conclusions Co-infection with TB and Bartonella presenting with lymphadenitis is unusual. Cat-scratch disease can be a rare clinical presentation of Bartonella infection in patients with AIDS, but coexistence of bartonellosis and paradoxical IRIS has never been reported before. However, physicians treating people living with HIV should be aware of this potential concurrence. Early testing for Bartonella infection could be offered in patients with TB and HIV co-infection in case of acute deterioration or partial response to treatment, especially if they have a history of cat exposure, since clinical picture can be indistinguishable.

In 2020 we suffered from a major global pandemic caused by the SARS-CoV-2 coronavirus. Efforts to contain the virus include the development of rapid tests and vaccines, which require a ready supply of viral proteins. Here we report the production of two SARS-CoV-2 proteins by transient transformation of tobacco, leading to high expression within three days, and subsequent purification of the intact proteins. Such efforts may help to develop testing resources to alleviate the major impacts of this global pandemic.

Several yield-related traits selected during crop domestication and improvement1,2 are associated with increases in meristem size3, which is controlled by CLE peptide signals in the CLAVATA-WUSCHEL pathway4-13. Here, we engineered quantitative variation for yield-related traits in maize by making weak promoter alleles of CLE genes, and a null allele of a newly identified partially redundant compensating CLE gene, using CRISPR-Cas9 genome editing. These strategies increased multiple maize grain-yield-related traits, supporting the enormous potential for genomic editing in crop enhancement.