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Mutations in IDH genes occur frequently in acute myeloid leukemia (AML) and other human cancers to generate the oncometabolite R-2HG. Allosteric inhibition of mutant IDH suppresses R-2HG production in a subset of patients with AML; however, acquired resistance emerges as a new challenge, and the underlying mechanisms remain incompletely understood. Here we establish isogenic leukemia cells containing common IDH oncogenic mutations by CRISPR base editing. By mutational scanning of IDH single amino acid variants in base-edited cells, we describe a repertoire of IDH second-site mutations responsible for therapy resistance through disabling uncompetitive enzyme inhibition. Recurrent mutations at NADPH binding sites within IDH heterodimers act in cis or trans to prevent the formation of stable enzyme–inhibitor complexes, restore R-2HG production in the presence of inhibitors, and drive therapy resistance in IDH-mutant AML cells and patients. We therefore uncover a new class of pathogenic mutations and mechanisms for acquired resistance to targeted cancer therapies. Significance: Comprehensive scanning of IDH single amino acid variants in base-edited leukemia cells uncovers recurrent mutations conferring resistance to IDH inhibition through disabling NADPH-dependent uncompetitive inhibition. Together with targeted sequencing, structural, and functional studies, we identify a new class of pathogenic mutations and mechanisms for acquired resistance to IDH-targeting cancer therapies. This article is highlighted in the In This Issue feature, p. 1

To report frequency and timing of adaptive radiotherapy (ART) and assess patient, disease, and treatment-related characteristics potentially triggering the need for such adaptive replanning in head and neck squamous cell carcinoma (HNSCC).Medical records of HNSCC patients treated with definitive intensity modulated radiation therapy (IMRT) with or without concurrent systemic chemotherapy were reviewed retrospectively to identify patients undergoing image-guidance triggered adaptive replanning. Clinico-demographic characteristics of patients undergoing ART were compared with patients treated without adaptation using the chi-square test.Two hundred patients with squamous cell cancers of the oropharynx, larynx, or hypopharynx treated with definitive IMRT between 2014 to 2019 comprised the study cohort. Twenty-seven (13.5%) patients underwent adaptive replanning during treatment at a median of 17 fractions (inter-quartile range 14-24 fractions). There were no significant differences in the baseline patient (age, gender), disease (site of primary, staging/grouping), and treatment-related characteristics (dose-fractionation, chemotherapy usage) in patients undergoing ART compared to those treated without adaptation. Weight loss during IMRT emerged as a significant factor predicting the need for ART; patients having ≥10% weight loss from baseline were more likely to undergo treatment adaptation compared to patients with10% weight loss (p = 0.0002). There was variable impact of ART on dose-volume statistics of organs-at-risk such parotid glands and spinal cord.Image-guidance triggered ART for HNSCC is not associated with significant improvement in OAR dosimetry. However, weight loss during definitive IMRT can be a potentially useful trigger for identifying patients who are most likely to benefit from such adaptive replanning.

Malignant hematopoietic stem cells (HSCs) initiate the myelodysplastic syndromes (MDS) and drive treatment failure through their resistance to all non-transplant therapies. As a result, allogeneic stem cell transplantation (allo-SCT) is the only curative therapy for MDS. However, relapse remains the leading cause of treatment failure after allo-SCT. Improved tools to predict relapse in this setting are necessary to allow for pre-emptive therapeutic interventions, which may be more effective when the burden of disease is still low. Given prior evidence that HSCs serve as the functional unit of resistance to non-transplant therapies, we asked whether relapse after transplant originates from MDS HSCs, and whether their persistence can predict relapse. To overcome the limiting number of HSCs available in clinical bone marrow (BM) samples, we adapted a workflow developed for assessment of cell-free DNA and utilized a hybridization capture-based targeted sequencing panel covering 260 myeloid malignancy-associated genes. Unique dual index primers (UDIs) were utilized to tag input DNA, improving PCR duplicate identification, which overcome issues with amplification bias typically faced by low-input sequencing. This ultimately allowed us to consistently capture evaluable read depths from as few as 10 sorted cells. We assembled an initial cohort of 21 patients who underwent allo-SCT for MDS or secondary acute myeloid leukemia. Inclusion criteria were follow-up time greater than 1.5 years (or relapse in this timeframe), BM sampling prior to Day+120 post-transplant and relapse, and biospecimens allowing for sorting of greater than 10 HSCs. We sequenced sorted CD34+CD38-CD45RA- HSCs and multipotent progenitors (MPPs), CD34+CD38- CD45RA+ lymphoid-primed multipotent progenitors (LMPPs), and CD34+CD38+ progenitors, as well as bulk BM. With a median follow-up of two years, 9 of the 21 patients relapsed, with an average time to relapse of 362 days. Detection of disease mutations in HSCs/MPPs in any BM at D+30-D+120 post-transplant was 100% specific and 88% sensitive for relapse, showing improvements in both metrics over bulk BM assessment (22% sensitive and 66% specific), despite far lower cell input and read depth. Average time from detection to relapse was 6.9 months. In patients destined to relapse, disease mutations are often present in HSCs at a variant allele frequency of greater than 45%, while simultaneously undetectable on high-depth sequencing of bulk cells (>400x coverage). While even higher depth error-corrected sequencing bulk BM could likely detect such mutations, it would require >20x the sequencing depth, and could not identify the involved cell populations. In conclusion, we show for the first time that relapse of MDS after allo-SCT is driven by failure to eradicate MDS HSCs. Detection of MDS HSCs early post-transplant is highly predictive for relapse and opens new doors for pre-emptive interventions to prevent relapse. These findings are being validated in an independent cohort of 46 patients and updated data will be presented at the meeting. Citation Format: Benjamin Kroger, Yi Huang, Prapti Patel, Aimaz Afrough, Gurbakhash Kaur, Larry Anderson, Farrukh Awan, Praveen Ramakrishnan, Kunal Verma, Russell Vittrup, Robert H Collins, Madhuri Vusirikala, Yazan F Madanat, David Sallman, Carmelo Gurnari, Jaroslaw Maciejewski, Roni Tamari, Stephen Chung. Less is more: Ultra-low input sequencing allows for evaluation of stem cells as a predictor of post-transplant relapse in the myelodysplastic syndromes [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A23.

In vitro dosimetric verification prior to patient treatment has a key role in accurate and precision radiotherapy treatment delivery. Most of commercially available dosimetric phantoms have almost homogeneous density throughout their volume, while real interior of patient body has variable and varying densities inside. In this study an attempt has been made to verify the physical dosimetry in actual human body scenario by using goat head as “head phantom” and goat meat as “tissue phantom”. The mean percentage variation between planned and measured doses was found to be 2.48 (standard deviation (SD): 0.74), 2.36 (SD: 0.77), 3.62 (SD: 1.05), and 3.31 (SD: 0.78) for three-dimensional conformal radiotherapy (3DCRT) (head phantom), intensity modulated radiotherapy (IMRT; head phantom), 3DCRT (tissue phantom), and IMRT (tissue phantom), respectively. Although percentage variations in case of head phantom were within tolerance limit (< ± 3%), but still it is higher than the results obtained by using commercially available phantoms. And the percentage variations in most of cases of tissue phantom were out of tolerance limit. On the basis of these preliminary results it is logical and rational to develop radiation dosimetry methods based on real human body and also to develop an artificial phantom which should truly represent the interior of human body.

Purpose: Evaluation of setup accuracy in kV-orthogonal portal imaging (OPI)-based and kV-CBCT-based radiotherapy treatment and to find out the necessity of cone-beam computed tomography (CBCT) compared to OPI. Materials and Methods: A retrospective study was carried out on 30 patients, who received radiotherapy to the Brain, Head and Neck, and Pelvis. In the OPI technique, anterior-posterior and right-lateral portal images were taken by the On Board Imaging (OBI) system and were superimposed on the reference images. Similarly, in the kV-CBCT technique, CBCT was performed by the OBI system and CBCT images were superimposed on the reference CT images. A total of 150 comparison sets of kV-OPI and kV-CBCT images were analyzed and evaluated. Shifts in the Lateral, Longitudinal, and Vertical directions were noted in both techniques. The iso displacement vector (IDV) was calculated for all imaging. Results: The mean IDV (in cm) are found to be 0.3395 (SD: 0.1477) and 0.3088 (SD: 0.1593) in cases of the brain, 0.4266 (SD: 0.1511) and 0.3666 (SD: 0.1533) in cases of the head and neck, and 1.0339 (SD: 0.5893) and 0.9498 (SD: 0.6047) in cases of the pelvis for the CBCT and OPI techniques, respectively. The P values were 0.3201, 0.0515, and 0.4829 for the brain, head and neck, and pelvic cases, respectively. Conclusions: There is statistically no significant difference between both the imaging techniques. As the dose delivered by the CBCT technique is higher than that by the OPI technique, from the socioeconomical and radiation safety point of view, the OPI technique is possibly better than the CBCT technique. Hence, it can be concluded that CBCT is not a mandatory technique compared to the OPI technique in routine brain, head and neck, and pelvic cases, except in those cases where better information about interfraction movements of soft tissue is necessarily required for positioning of the target, as is the case in prostate carcinoma.