Table 7 A summary of purported mechanisms correlating specific gene deletions beyond NF1 to phenotype in NF1 deletion syndrome

Cardiovascular malformations

Includes: Pulmonary stenosis, atrial/ventricular septal defects, valve defects, hypertrophic cardiomyopathy, and patent ductus arteriosus.

SUZ12

SUZ12 is known to be deleted within NF1 deletion syndromes and shown to be expressed during a short period of cardiac morphogenesis within the heart atria. Cardiac cell

fate is conditioned by PRC2 recruitment through a variety of lncRNAs, including Bvht, Fendrr, Carmn, Chaer, Ppp1r1b51, and HBL1.

Additionally, heterozygous flies with a Suz12 loss of function mutant allele show impaired expression of various Hox genes (e.g. Ubx and Abd-B) required for appropriate cardiogenesis.

Haploinsufficiency of this gene may thus contribute to observable cardiovascular malformation.

Venturin et al. 2005 [69]

Wang et al. 2022 [37]

ADAP2

Deletion of ADAP2 within NF1 deletion syndrome debilitates its role during fundamental phases of cardiac morphogenesis, resulting in defective heart looping and valvulogenesis.

Venturin et al. 2014 [52]

Higher malignant potential

UTP6 (HCA66)

Shown to selectively modulate Apaf-1-dependent apoptosis, resulting in increased downstream caspase activity following cytochrome c release from the mitochondria. HCA66 depletion severely impaired apoptosome dependant apoptosis, thus HCA66 haploinsufficiency has been proposed to render NF1 deletion patients’ cells less susceptible to apoptosis and more amenable to developing malignancy.

Piddubnyak et al. 2007 [63]

ATAD5

Mice exhibiting ATAD5 haploinsufficiency display a high magnitude of genomic instability and DNA damage hypersensitivity, with the ATAD5 protein shown to hold a regulatory role in stabilizing stalled DNA replication forks. Somatic mutations within gene have also been identified within sporadic human endometrial tumours as well as breast and ovarian tumour cell lines, thus haploinsufficiency of this purported tumour suppressor gene could contribute to MPNST pathogenesis.

Bell et al. 2011 [48]

Kuchenbaecker et al. 2015 [49]

SUZ12

Genetic analysis within MPNSTs commonly identifies bi-allelic inactivation of SUZ12, suggesting of a possible tumour suppressor function. This function has been hypothesized to involve the SUZ12 protein’s role within the Polycomb repressive complex 2 (PRC2), which epigenetically regulates genes known to organise cell cycle progression, stem cell self-renewal,

cell fate decisions and cellular identity.

De Raedt T et al. 2014 [36]

MIR193A & MIR365B

These microRNA genes encode mature miRNAs such as miR193a-3p and miR193a-5p with well-known tumour suppressor functions. These have been demonstrated to exhibit downregulation across a multitude of malignancies from breast cancer cell lines to hepatocellular carcinoma and non-small-cell lung cancer. This observation has yet to be validated within MPNSTs; however, highlighting an avenue for future investigation.

Salvi et al. 2013 [65]

Yang et al. 2013 [66]

Yu et al. 2015 [67]

Tsai et al. 2016 [68]

RNF135

RNF135 overexpression has been shown to inhibit malignant potential of tongue cancer SCC25 cells, promoting expression of tumour suppressors PTEN and TP53.

Jin et al. 2016 [60]

COPRS

COPRS is involved in regulation of myogenic differentiation, which may, in haploinsufficiency contribute to oncogenic dysregulated differentiation patterns. Whilst COPRS has been shown to be overexpressed in some MPNST tissue samples; this finding is inconsistent across the literature with low expression additionally recognised.

Kehrer-Sawatzki et al. 2017 [64]

Overgrowth in stature

RNF135

Genomic analysis of individuals with overgrowth phenotypes of unknown cause has highlighted RNF135 haploinsufficiency to contribute to phenotypes of overgrowth, facial dysmorphism and possibly learning disability. As RNF135 is found within the NF1 deletion region at 17q11 and all three of these phenotypes are readily observable within NF1 deletion syndrome, RNF135 has been suggested to underlie this correlation.

Douglas et al. 2007 [57]

SUZ12

A SUZ12 missense mutation has been identified in a patient exhibiting a Weaver-like syndrome that was associated with overgrowth, thus SUZ12 has been suggested to contribute to this phenotype in NF1 deletion syndrome. Additional reports of patients with Imagawa-Mastumoto syndrome due to SUZ12 pathogenic variants contribute to this hypothesis.

Imagawa et al. 2017 [28]

2023 [29]

Intellectual disability

OMG

The encoded OMGp is central to regulation of synaptic plasticity and possibly neurogenesis; dysfunction of which have both been correlated to intellectual disability. Haploinsufficiency may therefore contribute to the significantly lower full scale intelligence quotient observed in patients with deletion syndrome compared to patients with intragenic NF1 mutations.

These may form additive effects with RNF135 and NF1 haploinsufficiency. Indeed, the former has been linked to proliferative ability of neural stem cells, whilst neurofibromin is established as an important Ras regulator in interneurons influencing hippocampal-dependent learning.

Martin et al. 2009 [61]

Bernardinelli et al. 2014 [70]

Oliveira & Yasuda. 2014 [62]

RNF135

Genetic screening of patients with various degrees of learning disabilities or autism spectrum disorder, in association or not with overgrowth, identified several truncating, missense, synonymous or intronic variants in the RNF135 gene. Comparison with control populations showed a significant over-representation of the p.Arg115Lys variant in the group with autism, with several homozygous patients.

Douglas et al. 2007 [57]

Visser et al. 2009 [58]

Tastet et al. 2015 [59]

SUZ12

Subunits of PRC2 are expressed in the central nervous system (CNS) and its progenitor cells. They have a pivotal role in the development of central and peripheral nervous systems. As neurological issues have also been observed in Weaver and other overgrowth syndromes, SUZ12 constitutes another candidate gene for causing intellectual disabilities in NF1 deleted patients.

Liu et al. 2018 [31]

Tatton-Brown et al. 2017 [21]

CRLF3

Human induced pluripotent stem cell (hiPSC)-forebrain cerebral organoid (hCO) models from type-1 deleted patients (“total gene deletion” TGD hCOs), like hCOs with NF1 intragenic mutations, show neural stem cells (NSC) hyperproliferation compared to non-mutated control hCOs, but they also show abnormal dendritic maturation not found in shorter atypical deletion (aTGD hCOs). A single deleterious CRLF3 missense mutation (c.1166T > C, p.Leu389Pro) was recurrently identified in NF1 children with higher SRS-2 scores for autism evaluation. CRLF3-inactivated hCOs have normal NSC proliferation, but abnormal maturation.

Wegscheid et al. 2021 [55]